Differences in the tranny as stated before
There is a phosphate coating on all the gears.
The shift cover does not have a reverse switch on it.
The cobra tranny has a roller pocket bearing on the main shaft instead of the 15 needle type bearing.
The input shaft is 5/8 inch longer than the 86-93 tranny.
5th gear has 2 bronze syncros on it instead of one.
I just got done tearing mine apart and replacing some stuff in it. 140,000 miles on the tranny and the inside of my case still looked brand new.
As long as you get a 94-95 gt or cobra model trans then its a direct fit. When you run into a problem is any other year tranny because the input shaft length