I wouldn't think the input shafts were different either... But there were 2 versions of both cars (saying you have a coupe and not a sedan). The prisim GSI had the 4age and the regular one had the 4af/e.
Have you checked to see if everything was assembled correctly and that when you push the pedal in the lever moves and actually contacts to pull the clutch away?
i know there were two versions of both cars i got my disc brakes and stuff of a prizm gsi but i drive a sedan corolla and the transmission i got was off of a geo prizm with a 4afe i was gonna get one of of the gsi that was out there but it had a 4 speed auto and i didnt want that
but the transmission is like halfway on the car its not all the way in which is why i think it has differant input shafts i was an idiot and didnt make sure and check the clutch disc before i put it on the car and started to put stuff back together
but my main question is how the crap can i get the transmission unstuck so i can make sure i have the right parts and everything