The axel support bearing housing is different between automatic and manual transmission cars.  On the engine side of the intermediate axle bearing support is a cast mark "A" or "M", for AT or manual transmission.  BE SURE YOU CHANGE THE BEARING SUPPORT if you convert from auto to manual trans.  That is to say, make sure the support has an M stamped on it if you're installing a manual transmission.

Dave says:
"The driver's side axle is slightly longer on the 5spd." 
He also points out that the two wires to the automatic's neutral safety switch have to be shorted together to allow the car to start.