My train of thought is weird and cluttered but here it is.
Is the tranny being supported on a trans jack?
Try messing with the output shaft with your hand while putting the trans in.
When the trans was off, was the car started at any time? If so then you have to realign the clutch.
What year is your car? If you have a fox, and are using a 94/5 t-5 the inputshaft is longer.
Sorry for the cluttered post