Best way to rebuild a 9000 5-speed: Contact thesaabsite.com and order a rebuilt unit.  They sell Eriksson's rebuilts at the best price you can find.  All told, it's in the neighborhood of $1500.  Sounds like a lot, I know, but what you get is a sparkling clean, ready to install trans that needs only a slave cylinder and a mount.  It'll look a lot better than anything you can do, and it will be right.  Can you rebuild it yourself?  Maybe.  Probably, if you're diligent, resourceful, careful, determined, experienced, and have the manual.  Personally, I failed - I made every rookie mistake that could be made, probably.  I feel sure that I could succeed next time, but there probably never will be a next time (I would prefer to think that you don't get more than one 9K 5-speed failure in a lifetime!)  If you want to give it a shot, have at it; worst case, you'll throw away $500 or so and a couple of weeks of your life.  Be advised, though, that with another grand you could be up an running with an Eriksson rebuilt before that couple of weeks went by!  I don't regret having tried, because it was fascinating; educational; challenging.  And as I said, having paid the price of making all the mistakes and ultimately failing, I could do it now.  Hell, you could bring me all the parts in a box and I could probably put it together correctly.  The adjustments are tricky though.  And it's pretty easy to screw something up.  It's really worthwhile to buy an Eriksson rebuilt!  Eriksson is one of the finest, most honest, helpful and upstanding outfits I have ever dealt with.

Here's a link to a very good pictorial of a 9K 5-speed partial teardown: http://homepage.ntlworld.com/home01/gearbox/index.html.  Mr Haydon had much, much better tools to work with than I had; my description is more for those of you who don't have much in the way of pullers.  Also, he went in specifically to replace the second gear synchronizer ring, which involves only partial disassembly of the output shaft gear cluster, without removing the input shaft, whereas I tore mine completely down.  He succeeded, by the way; I failed.  I ended up ordering an Eriksson rebuilt.  I think I could rebuild one completely now, but I made too many rookie mistakes the first time around, and they finally caught up with me.  I'll just try to point out the pitfalls and high points that I encountered.  If you need specific help, feel free to e-mail me.  I'll say this:  It takes either a stout or a foolish heart to attempt a 5-speed rebuild if you have no special tools.  That having been said, though, I would not be afraid to attempt it again; having been armed with all that I learned from my failure, I do think I could pull it off now.

I originally thought that I would document the trans rebuild rebuild in its entirety, but I decided against it.  If you don't have the manual, then you shouldn't try it.  I could devote several megabytes to it here, but I don't think it's worth it.  Truth be told, my experiences indicate that even the Saab dealers resort to installing a rebuilt unit, rather than trying to rebuild themselves.

To disassemble and reassemble the 5-speed successfully, you either need some highly specialized tools, or you need to have some really good pullers to start with, or you need to be very inventive and determined.  Since I could find precious little in the way of special pullers, I went the latter route.  Bear in mind that in the absence of special tools, you often have to get a bit crude.

WARNING: Gears are unforgiving!  When you're turning any exposed meshing gears, and particularly when you're tightening nuts or pulling gears down, keep your hands clear of the gears!  DO NOT hold a gear with your hand while tightening or turning.  I made the mistake of holding a gear while pulling a matching gear and bearing onto one of the shafts - the transmission was locked, but one gear slipped and my thumb was instantly pulled into mesh between the two 5th gears.  Fortunately, the wrench slipped off simultaneously and the gears spat my thumb back out the same way it entered.  I was extremely fortunate that my thumbnail escaped, but the side of my thumb was badly mangled.  In a flash.  Two hours at the emergency room, and a few stitches.  Coulda been a lot, lot, whole lot worse ... I shudder to think, because, trust me, it was really ugly as it was.  As I told my buddy Bob Davis, transmissions have soul, because they're complex machines.  But gears, they just have purpose, and God help you if you get in the way of that purpose.  BE CAREFUL!

Disassembly

bulletTypically, in order top lock the transmission for certain operations, you'll engage either 3rd gear or 4th gear so that you can simultaneously engage 5th gear (once its shift fork has been removed) .  How to select gears
bulletSynchronizer hub assemblies: All of the synchronizer hubs have three sets of odd teeth that are a little higher than the rest; the corresponding valleys in the sleeves are a bit deeper to accommodate  them.  The three odd sets are spaced at 60 degree intervals and will be midway between the three sets of bosses/slots.
bulletTo remove the nut from the output shaft (after removing the end cover and 5th gear selector fork)
bulletPress the sleeve down to engage 5th gear and lock the transmission
bulletPry up the three crimps on the output shaft nut 
bulletRemove the nut
bulletWhen reassembling, replace this nut with a new one
bulletBefore splitting the case. be sure to remember to remove the reverse gear shaft support bolt from the side of the transmission case
bulletHalf of the case must be pulled off (you're actually pulling a bearing off the shaft by pulling the case and its bearing race).  You may use a small puller to remove 5th gear first, or you may pull it off along with the bearing and case.  If you decide to remove 5th gear separately:
bulletA "split dish" type puller might do the trick - you can get them at places like Harbor Freight for around $20.  
bulletSears sells a very nice, sophisticated 3 jaw puller that will do it, if you get the smallest size.  It's $50 though.  And you'll have to ignore the statement about voiding the warranty, and use a pair of ViceGrips or similar to power the jackscrew hard enough to do the job. 
bulletAs previously stated, you can just leave the gear and pull it along with the case and bearing, although the added resistance of the press fit of the gear might make things a bit more difficult in the next step, and would increase the risk of stripping screw holes in the case.  I would advise pulling  the gear now if you have the means to do it.  Be careful to get sufficient purchase on the gear to avoid breaking off teeth.
bulletRemove the case half - the first big challenge!
bulletThe output shaft's bearing is pressed onto the output shaft, and the bearing race is in the case.  That means that you have to pull the case upward to pull the bearing off the shaft.  It's not a vicious press fit - it's tight enough, but the real problem is how to get hold of the case to pull it off.  Let me say right here that you do not want to try to pry the two case halves apart.  First, you'd have to pull the case initially to get anything in there anyway.  Second, You might well break the case.  Third, you'd ruin the two mating surfaces, and those have to seal without the aid of a gasket.  So we have to pull the case half off, bringing the bearing with it.  Saab's special tool is essentially a D-shaped ring that is welded onto a bolt.  Two of these screw into bolt holes in the case on opposite sides of the output shaft.  Now you center a two-jaw puller on the end of the output shaft, catch the rings with the puller fingers, and pull the case up and off.  It takes a pretty long puller with a fairly wide span, and 2-jaw pullers aren't very common.  Even a steering wheel puller doesn't have enough span to do the job.
bulletAn alternative is to take a stout steel bar, lay it across the end of the output shaft, drill two holes approximately 4 3/4" apart, run long (5 inches or so) bolts of the proper metric size and thread down into the threaded holes in the case on opposite sides of the shaft, and tighten them into the holes to pull on the case.  Put anti-seize compound on the bolt threads, and tighten them alternately and slowly.  Put a 2X4 against the case at the join line and whack it with a hammer - do this all the way around. Tighten a turn or so, whack the case - repeat until the case halves separate; thereafter, you can cease the whacking and continue tightening the bolts.  The bolts will bottom out after 5/8" or so of travel, so pay attention or you'll over-tighten at the end of their travel and strip the threads in the case (due to flex, compression, what have you, the case will probably only move about half that distance before the bolts bottom out).  Instead, back the bolts out at that point, put a piece of shim material between the cross piece and the shaft end, and go at it again.  Two or three iterations will get the case off.  I was fortunate enough to find an old piece of a trailer hitch assembly - it was 1/2" steel and had holes that were perfectly spaced for the bolts.  
bulletAnother option would be to use longer bolts and the same cross piece with a hole drilled mid way, large enough for a steering wheel puller jackscrew.  You could put he puller plate beneath the cross piece and then run the jack screw down to the output shaft, install the long pull bolts, then jack the case out using the jackscrew rather than the bolts.  Long bolts can be found in a good steering wheel puller set, although they won't be long enough for the second option.  A good bolt store is your best bet.
bulletRemoving the shifter mechanism
bulletEngage fourth gear.
bulletRemove the bolt that holds the assembly
bulletLift the mechanism slightly so the guide sleeves come out of their positions
bulletRemove the guide sleeves
bulletPull the mechanism backwards toward the differential and swing it out slightly
bulletLift the mechanism out
bullet Removing the input shaft, complete with gears - the second big challenge!
bulletBefore starting, be advised that the second gear synchronizer assembly will fly apart if you pull second gear too far in front of the synchronizer assembly.  It's easy to reassemble, but take care not to lose any of the three little "beans" (metal pieces about the size of a pinto bean)
bulletThe input shaft would lift right out if not for interference between its lower bearing and first gear on the output shaft.  You can remove the interference either by completely disassembling the output shaft gear stack piece by piece, or by raising the entire stack of gears on the output shaft about an inch.  If you have a very long two-arm puller, the latter is a piece of cake, but you don't have that puller, do you?  The only thing offering resistance on the output shaft is a spacer bushing on second gear - it's a fairly light press fit.  As such, you can actually lever and pry the gear stack up from the bottom.  We started with screwdrivers, progressed to chisels, and ended with cats claws (sort of a short, flat pry bar).  I eventually discovered that two of these on opposite sides are just the thing, although you should use screwdrivers at first to get enough room under first gear.  This is a crude way of doing business, but if you work carefully, it works just fine.  So, lift the output gear stack about an inch, then tilt the input shaft away from the interference and lift it out, complete.
bulletNow you can finish levering the output gear stack up - after about two inches it comes free.  
bulletHave a piece of 1/2" semi-rigid foam pipe insulation about 10"" long handy - it makes a very nice snug fit to keep the gear stack on.  Picture.
bulletRemoving the output shaft bearing race (it's pressed into the case): 
bulletFirst, remove the bearing retainer plate.  The bolts are very shallow T-30 (I think) Torx head.  They're tight, and you can strip the Torx socket out of them in a heartbeat if you're not very careful.  You'll need a Torx bit with a 3/8" drive, and you should fit it to a 3/8" breaker bar.  Note that there's about a 2" moment arm between the top of the breaker bar and where the tool meets the bolt - you do not want the tool to cock sideways and ride up out of the bolt at an angle, because that will strip it out.  So insert the tool into the bolt head, lean very hard directly on top of the tool, and push the business end of the tool in the opposite direction to which you're pulling on the handle end of the breaker bar.  In other words, work hard at keeping the tool vertical while you press it down and turn it.
bulletNow you can use the nut on the end of the output shaft to pull the whole shaft and race out.  First, install four case bolts into the four center holes for the bearing plate - just a couple of turns each.  Now lay the bearing plate on top of them.  Now cut a small piece of 3/4" plywood and hole-saw a 1 3/4" to 2" hole in it so you can put it over the shaft and on top of the bearing plate (spreads the load on the bearing plate).  Now find something to act as a plate at the nut end (I used a weight from a dumb bell set).  Now put the end plate over the shaft, screw the nut a turn or two onto the shaft and measure the distance between the plywood base plate and the end plate.  Cut a length of PVC pipe to fill that distance, install it between the bottom and end plates, install the nut, then tighten it down to pull the shaft out (you'll have to use a screwdriver to lock the differential gear).  If the nut bottoms out before the bearing race comes free, back out, shim and go at it again.  Here's a picture of what I used.
bulletIf you want to pull the differential assembly out of the case, it's pretty easy to do. ¢
bulletNOTE!  If you want to remove the differential assembly, but don't intend to disassemble the differential assembly itself, then be sure to keep the splined driver gears centered in their openings.  They can rotate quite a ways before they fall out, but once they do fall out, it's quite a challenge to reassemble them correctly.  To reassemble correctly, they both have to be rotated 90 degrees out of their sockets, positioned exactly opposite one another, then rotated into position while meshing with the differential gears.  It's much more difficult than it sounds if you've never done it before!
bulletFrom the outside of the case, remove the 5 bolts that secure the output drive cup assembly
bulletTap the driver assembly to loosen it, then pull it out
bulletCollect the shims - bag 'n' tag
bulletRotate the ring gear until one of the two the cutout arcs aligns with the output boss on the case
bulletAt this point, the manual says to just lift the gear out, but I had to ã pry mine out - it just neede¦ some persuadin¥.  If you òemove the speed®meter §rive gear, the ²ing gear will léft out without ënterference.
bulletAt this point you could pull some bearings and tap out some bearing races and seals, but essentially, the transmission is completely disassembled.

 

Now that it's apart

bulletWash everything down thoroughly with a good solvent.  I hope you're smart enough to not use gasoline - that stuff is way too dangerous to be used as a parts cleaner.  Kerosene worked well for me.
bulletDisassembly of the input shaft is pretty simple once you get the bearing off the snap-ringed end.  Even with Saab's special tool, the bearing is destroyed by removal, so don't worry about destroying it.  Break up the roller cage with a screwdriver/pliers/whatever.  That will leave just the bearing housing.  You can get a "split dish" type puller at Harbor Freight that will move the housing far enough to get a puller on it.
bulletBe sure to inspect the snap ring on the input shaft, in front of the 3 - 4 synchro hub; this appears to be something of a common failure point in the 94 and later transmissions.  If there is no thrust washer installed between the snap ring and the hub, I recommend sending it to Eriksson and letting them do the modification to install it.  If you send them everything, they'll do the mod, press on new bearings and send it back reassembled.  The machine and assembly work were only $65 when I had it done.
bulletInspect the synchro rings carefully for any wear.
bulletAs far as I can recall, all bearing races can easily be tapped out with a hammer and drift.  They can be tapped into position, but a press is definitely preferred.  You might want to leave press work to a machine shop.
bulletFor the input shaft bearing in the gear case end (the part that you pulled off), you can start it by tapping it in with a hammer, then you can pull it in using the bearing plate and four screws.  DO NOT PULL THE BEARING COMPLETELY DOWN - leave some end-lash so you can make the final end-play adjustment after reassembly.

 

Reassembly

bulletIf the differential assembly was removed from the case, make sure that the splined gears are aligned exactly opposite each other.  In other words, make sure that the axels can be plugged into the splines once the differential assembly is installed.  As noted above, the assembly can fall apart and be reassembled such that the gears fit into the assembly, but  not be aligned such that the axels can be plugged in.  Just make sure all is well before installing the assembly into the case.
bulletAlign one of the two cutouts in the ring gear with the boss in the case.  Push the ring gear toward the boss and downward into the case.  If the speedometer drive gear has not been removed, there will be some interference to overcome.
bulletNOTE: When installing the output driver shafts (the manual calls them "bearing supports", I think), they can bind up.  Grease the splines first.  Pull the assemblies into place by tightening the bolts a little at a time, in a criss-cross pattern.  Tap on the end of the driver cup or splined axel (depending on which side you're installing) often as you go.  Also, rotate the output shaft occasionally to keep things freed up.
bulletInstall the output shaft
bulletPlace the end of the shaft into the hole in the case
bulletthe pinion gear on the end of the shaft will mate with the ring gear on the differential
bulletPosition the bearing race, tapered side toward the bearing, and tap it gently all the way around to get it started.  You can then tap it down most of the way with a hammer (manual says "plastic hammer", or you can install the bearing retainer plate and pull the race into place by alternately tightening the three central screws on the retainer plate.
bulletThe manual says to install the bearing plate and tap it down with a plastic hammer and a tube that fits over the shaft - again, you can do that, or pull it down with the screws.
bulletNote: Don't Loctite these, just torque them down.
bulletTorque: Three center screws: 30 ft-lb; lone outer screw: 20 ft-lb
bulletTool: T-40 Torx
bulletIf you're working alone, you might have to straddle the case and hold it with your knees to keep it from turning as you apply the torque
bulletAlways pull the torque wrench smoothly but assertively -  don't jerk it, but don't try to pull very gently and slowly either
bulletWhen done, the shaft will have a lot of wobble room - that is, the bearing race will not be pulled down snug against the bearing.  It's tempting to remove the plate and drive the race on down as gar as it will go, but don't do that.  The manual says to press it into place with the bearing plate, and that's what they mean.  The end play will be adjusted by crushing the crush sleeve later on, toward the end of the assembly.
bulletAssemble the 1 - 2 synchro assembly with 1st and 2nd gears; use three medium sized cable ties to "cross-strap" the assembly together
bulletGo under one side of 1st gear, then cross over to come over the other side of second
bulletHolds assembly together and allows installation on the shaft
bulletPut the assembly onto the output shaft and leave it where it comes to rest (don't force all the way down)
bulletOrient the cable ties that retain the synchronizer assembly so the bottom of the strap is on the outside (so it won't interfere with the input shaft gear stack when it's put into position)
bulletAdd third gear and the spacer sleeve (the longer sleeve, not the crush ring)
bulletStand a socket on end, to act as a stand-off between the case and 1st gear (catch the bottom of 1st gear) - you want an inch to 1 1/2" of space between the case and the bottom of 1st gear
bulletPush the gear stack down until it contacts the stand-off. 
bulletYou might need to use a length of PVC pipe to tap third gear down flush (you're actually tapping the second gear spacer down)
bulletYou'll need to cable-tie the two shafts together, so fix a large cable tie (18" or so) in a loop, or chain several smaller cable ties together
bulletPut the input shaft into the case.  Align 1st, 2nd and 3rd gears on the two shafts, then cable tie the two assemblies together
bulletPush and tap the gears down onto the output shaft until you can fit a new clamping sleeve ("crush sleeve") and 4th gear
bulletThat's a NEW clamping/crush sleeve, not the old one
bulletThe MACHINE MARKS on 4th gear face UP, toward you
bulletCut and remove the cable ties holding the synchro stack together
bulletNow use the nut to pull the gear stack all the way down onto the output shaft
bulletThe fit gets progressively tighter the further you press the gears down
bulletFind an end plate - a small square of 1/4" plywood will do
bulletDrill or cut a hole in the center, of at least 1" diameter
bulletFit the end plate onto the shaft, then thread the nut a couple of turns onto the shaft
bulletMeasure the distance from the bottom of the end plate to the top of 4th gear, then cut a piece of PVC pipe to that length
bulletRemove the nut and plate, install the PVC pipe, reinstall the plate and nut, then turn the nut to pull the gear stack down onto the shaft.
bulletYou'll need to hold one of the gears to keep the shaft from turning - be careful not to get flesh between the gears
bulletAs the press becomes progressively tighter, you'll need to push the 1 - 2 synchro sleeve down to engage 1st gear so that you can then jam 1st gear with a screwdriver (something softer would be better) where the input and output gears meet.  You'll also have to push the input shaft toward the output shaft.
bulletPull the stack down until the 4th gears on both stacks are even with each other
bulletNOTE: "Even" varies with the perpendicularity of the stacks, so do try to push the stacks into alignment before you judge the evenness of the gears.
bulletYou'll have to use some pretty good torque to get there.  Don't get crazy about it to the extent that you crush the sleeve - just get them reasonably even with each other (within 1/32" or so)
bulletInstall the reverse gear assembly
bulletBut FIRST: Make sure that the aluminum shaft support is properly aligned on the steel shaft
bulletInsert a case bolt into the aluminum support and make sure that it can be screwed into the threaded hole in the shaft
bulletThe end of the shaft should be flush with the end of the aluminum piece
bulletIt can rotate out of alignment as well (although it's a loose press fit)
bulletTHERE ARE NO THREADS IN THE ALUMINUM SUPPORT, nor are there any in the case where the bolt goes - it's the hole in the shaft that's threaded, so it has to align properly in the aluminum support piece.  
bulletMine got out of alignment and it took forever to figure out where the hell the threads went, because I expected them to be in the aluminum piece. 
bulletAlign the hole in the exposed end of the shaft (opposite the aluminum support piece) with the channel in the case
bulletLift the input shaft slightly and slip the reverse shaft into its hole in the case
bulletMake sure that the hole for the aluminum support piece faces out toward the case
bulletInstall the gear change mechanism  (relax, this is easier than it looks)
bulletPut the 1 -2 synchro sleeve in the neutral position (the manual says to engage 2nd, but neutral worked better for me)
bulletEngage 4th with  the 3 - 4 synchro sleeve (push and lock upward)
bulletPosition the case such that the differential is on your left and the input shaft is to your right.
bulletMake sure the 1st gear selector fork is pushed as far down on the shifter mechanism as it can go.  Looking at the assembly with the large 1 - 2 shift fork on the right, and the boss with the hole hanging down on the left:
bulletLeft-most selector about 1/8" from the base of the assembly, no notches in the shift rod visible
bullet2nd from left: 3/8" from base, no notches visible
bullet2nd from right (3 - 4 selector): 3/8" from base, half the notch in the shift rod visible
bulletRight-most (1 -2 selector):  Bottomed against the base
bulletFind the case hole that is just to the left of the serial number plate (just to the right of the alignment sleeve).  It's in the center of the case, at the bottom, with the ring gear on the left; it's also approximately in line with the inner end of the shifter shaft bushing (inside the case).
bulletAlign the boss with the hole in it - the thing that hangs down from the base of the shifter assembly - with that hole, angle the 1 - 2 shifter fork downward and guide it into the groove in the 1 - 2 synchro sleeve.  Push the assembly toward the gear set and rotate it to the right - theoretically, the forks should slide onto the sleeves and the assembly should rotate right into place.  Sometimes it works like magic, and sometimes it doesn't.  Slightly cocking the assembly upward on the right side might help.
bulletPush the 1 - 2 sleeve down to engage 1st and press the selector assembly against the case
bulletInstall the two steel sleeves in their holes, and install the long bolt into the left-most hole, then snug it down
bulletPry the 1 - 2 synchro sleeve up into the neutral position
bulletInstall the reverse gear lever
bulletSlip the left end of the lever into its notch in the reverse shift selector lever, while guiding the left end of the oil plate into position under the edge of the gear change mechanism
bulletInstall the short bolt into the right end of the lever mechanism, and the other long screw in the middle (common to gear selector and reverse lever assembly).
bulletTighten all three 12 mm bolts to 20 ft-lbs.  
bulletTo improve access to the right-most and center bolts, you can pry the first gear selector up into the neutral position, then push the reverse lever down on the right side
bulletMy 1/2" drive socket still didn't fit well, so I used a 3/8" drive socket and a 1/2 to 3/8 adapter on the torque wrench
bulletInstall the reverse fork
bulletFit the reverse fork into the reverse sleeve, with the longer end of the tubular part facing up
bulletRotate it clockwise into position onto the end of the reverse gear lever
bulletInstall the reverse shift rod
bulletIt just kind of sits there (nothing appears to secure it)
bulletPry the left end of the reverse gear lever up to engage reverse gear
bulletInstall the main shift shaft
bulletFirst, lube both the shaft and seal lightly with grease
bulletNext, remove the "carrier" - the little piece that attaches to the shaft.
bulletNext, position the carrier
bulletThe long tang goes between the two shift plates in the shifter mechanism
bulletThe notch aligns with he lower end of the longer shift plate
bulletNow slip the rod through the seal and into alignment with the rounded bottom part of the carrier.
bulletPush the rod in until its threaded hole aligns with the hole in the carrier
bulletMAKE SURE THAT THE BIGGER END OF THE TAPER PIN FACES UP (nut faces down)
bulletRotate the rod 180 degrees if necessary
bulletInstall the T-40 bolt, then torque it to 20 ft-lb
bulletTEST THE GEAR SELECTION OPERATION - NOTE: Do not select gears by pushing on the synchro sleeves - USE THE GEAR SELECTOR SHAFT!  It is possible to engage a gear by pushing on the sleeve, such that the gear selector will be in the wrong position, which renders it inoperable.  Yes, I found this out the hard way, and had to split the case again to correct it.
bulletFirst, make sure that all of the shift selector slots are aligned
bulletThere's one on each shaft (3 steel, plus the brass 1 - 2 shift fork's slot)
bulletMake sure the 1 - 2 and 3 - 4 sleeves are centered in the neutral position
bulletOne of the other rods is connected to the reverse lever - pry it into position if necessary
bulletIt might be necessary to pry or tap the last rod (5th selector) into position
bulletGently grasp the selector shaft with Vice Grips and select each gear.  How to select gears
bulletUsing the selector shaft. engage 3rd gear
bulletAll the guts are now installed, and it's time to reassemble the case - this is your last chance to makes sure that:
bulletThe reverse gear shaft is properly installed
bulletHole in the reverse support hub faces out toward the case
bulletAnd a bolt can be threaded into the shaft through that hole
bulletAll the fasteners are tight
bulletThree 12 mm bolts that secure the shift selector and reverse lever assemblies
bulletT-40 screw that secures the carrier to the shift rod
bulletThere is nothing inside the case that isn't supposed to be there
bulletDirt
bulletMetal filings/shavings
bulletTools
bulletNuts, bolts, whatever
bulletThe shift selector is properly aligned
bulletThird gear engaged, with the shift selector in the notch
bulletAssemble the case halves
bulletMake sure the guide sleeves are installed in their holes
bulletThey should be in the clutch case (where the gears are), below the mating surface
bulletBefore applying sealant, test fit the gear case to make sure everything is aligned
bulletYou'll have to guide the gear case half over the shift rods
bulletWhen the case halves mate, make sure that you can see the hole in the reverse shaft support through the hole in the case
bulletIf not, remove the gear case and turn the support to align the holes, then test-fit again
bulletAlso, make sure that you can screw a case bolt into it
bulletIf not, see reverse shaft assembly alignment notes
bulletWhen alignment is confirmed, remove the gear case and apply Loctite 518 (Permatex 51813) anaerobic sealant to the mating surface of each case half
bulletTake care to not cover up the sintered metal vent piece in the gear case.  It's right about where the shift rods are (you can see a corresponding vent channel in the clutch case mating face)
bulletBrush the sealant out with a stiff brush
bulletThe manual says to allow a couple of minutes to dry, but whoever wrote that obviously doesn't know what anaerobic means!  In any case, it will take more than a couple of minutes to apply the stuff and brush it out.
bulletHow thick to apply it?  The manual says "sparingly".  A little goes a long way.
bulletGuide the gear case down onto the transmission
bulletMake sure the hole in the case aligns with the hole in the reverse gear support
bulletUse a Phillips screwdriver to align them, if necessary
bulletInstall one bolt beside each alignment sleeve
bulletJust barely snug, not tight
bulletInstall the bolt for the reverse shaft support
bulletTurn the transmission over and drive the guide sleeves up until centered in the case halves
bulletA small socket and perhaps an extension, tapped with a hammer, works well
bulletInstall the rest of the bolts
bulletSixteen, in all, plus one bolt and nut assembly
bulletThe manual does not show the bolt/nut assembly
bulletI'm not sure where it was supposed to go, but the guide sleeve that faces down when the transmission is installed made the most sense, so that's where I put it
bulletDO NOT install it in either of the larger holes that don't have guide sleeves installed
bulletThere's space between the two case halves there (no strength)
bulletI also had three studs with nuts on them, rather than bolts.  I saw nothing magic about them.  I assume they were originally intended as strap-down points for something, but they weren't used as such.  Just treat 'em as bolts.
bulletTighten all to 20 ft-lbs
bulletI used two tightening stages, generally working out from the center with a cross-tightening pattern.  The book doesn't mention any pattern.
bulletBE SURE NOT TO FORGET TO TORQUE DOWN THE REVERSE SHAFT SUPPORT BOLT
bulletPull the bearing onto the output shaft.  NOTE: Do not pull the bearing all the way down to its race - leave some end play.
bulletIn this step, you will have both 5th gears on their shafts, with 5th  engaged, to lock the transmission.  I made the mistake of only half way installing one of the gears - that's an excellent way to break gear teeth.  Get the gears fully in mesh so they can lock.  This is where I hurt myself when the 5th gear slipped while I was applying a lot of torque.  Engage 3rd gear, then push the 5th gear synchro hub down to engage 5th gear and lock the transmission.  Keep your hands clear of the gears while you're tightening.  WARNING: Gears are unforgiving - you do not want to find any part of your anatomy trapped between a set of gears!
bulletAssuming that you don't have Snooty Saab Tool 87 91 261, you'll have to get creative.
bulletThe nut on the end of the output shaft makes a nice puller, assuming that you can get the right spacers between it and the bearing.
bulletI started by putting a 1" box end wrench between the bearing and the nut, and pulled the bearing down until I ran out of threads
bulletThe wrench gave me a convenient resistance handle, and the friction also kept the shaft from turning.
bulletAfter that I found it necessary to lock the transmission by installing the fifth gears
bulletYou can tap the gear onto the output shaft using a hammer and socket/pipe/whatever
bulletStop driving when it gets to the bearing - it's not nice to drive bearings with hammer blows
bulletAt this point I assembled and installed the 5th gear and synchro hub onto the input shaft.
bulletSince there's too much space, I shimmed the assembly up with the handle of that 1" wrench.  This allowed the gears to mesh enough to lock the transmission when the synchro hub was pushed down to engage 5th gear.  Again, try to engage the gears comppletely or you'll break gear teeth.
bulletNOTE: You will probably have to tap the gear and hub onto the input shaft with a hammer.  Be sure to get it far enough onto the shaft that the hub can engage the gear and the hub.  And don't trust it not to slip - again, stay clear while torque-ing!
bulletNow that the gear is on the output shaft, we can pull it down with the nut.  Well, not quite ... there's some space on the underside of the nut, so it can't grip threads yet.  I put the nut on upside down and tightened it a few turns using Vice Grips.  Yes, it's crude, but I used the old nut, so who cares.
bulletWhen the gear has been pulled down sufficiently, you can put the nut on right side up and use an adjustable wrench or open end to tighten it on down.  A socket on a breaker bar works best because of the long lever arm (a 1 1/16" socket fits the nut).
bulletDO NOT PULL THE BEARING COMPLETELY DOWN TO THE RACE - leave a good bit of play for the final end-play adjustment.