The only manuals I can think of were the DOHC 3.4's, in which case the electronics would be all wrong for your '96 anyway...
There is no provisions to mount a clutch and pivot in a '96, that'd all have to fabbed and welded up...just for starters...cut the floor, properly install a shifter and cable, need to get a 1996 compliant manual ECM for a 3.1 (if it exists)...change wiring harnesses (powertrain)...etc...
I remember my friend had a Cavalier with a 3.1 and 5 spd, my auto '97 Lumina would run away from it...what are you trying to acheive?