Primary differences are the length of the shift levers, and the output shaft.
Other differences related to the transmission are shifter cables and brackets.
I've used a 90 trans in a 91 with stock cables. The cables just have to be adjusted a bit to fit right, but i don't remember which cable bracket i wound up using. It's not hard to put one in and run it. However, you have to either use a matching Tcase, or swap the output shaft (which is VERY easy).