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I am not 100% but I think Nothing. I know the newer units were built better as ford fixed some of the flaws in the E4OD. I do know there has been a couple threads on this however. You might try searching the old one for some more info.
I've searched, and read, only thing I found was the shift linkage is prob different between a 90-91 and 92up.
Reason I ask is, I sold(well sorta I guess) my 94 E4OD, the guy bought it for his 90, called me back and said, I won't worK for my pickup. The trans shop told him they are totally different between the two, and "We can't even make it work." WTF! As far as I knew, they where all interchangeable, up to 95, than its a simple plug change on the wiring harness to make it work.
On top of that, he said my trans is 8 inches shorter than his. I'm baffled.
Sorry, I misread the post. I thought his was the shorter trans. You are right the E4OD is huge.
If they are both 4x4 transmissions then they should be the same length.
If 4x2 then there may be differences in the tailshaft length.