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been discussed in great detail over on t00ners. Guts are the same (close enough) but housings vary.
A '90 unit going into a 91+ may or may not need the cable bracket, cables and shifter transferred from the '90 car. People have had mixed success, some get away with just the bracket. a '91+ going into a 90 needs all the extras every time IIRC
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).