I don't know all the differences, but the 1st difference I can think of would be bellhousings. The 2nd gen V8 and V6 engines have different boltpatterns, so the transmission would have to have a different bellhousing. I'm not certain, but I believe the 5R55E uses and integral (non-removable) bellhousing.
Also, in the 2nd gens (not sure about the 3rd gens), the V8 engine came mated to the 4R70W transmission rather than the 5R55E.
If this is about swapping transmissions from a 5.0 to a 4.0 (or vice-versa), I don't think it's easy.