I have a 91 and a 93 that both have good trannies, but I want to keep the 93 drivetrain as a spare and gut the rest of the jeep. My question is, besides the difference in the output shaft size, is there any other electronic or physical difference that would keep them from interchanging? (I'd be changing T cases as well)

 

I don't think you really have to worry about anything, output shaft size is the same it's the spline count you gave to be worried about 21 vs 23 but I believe that after 90 everything was 23 spline. 87 thru 90 was 21. Yes some had the input of the tcase longer but if both cases are the same is a swap.