The differences are many, first off the 1st gear ratio is 4.10, bearings, input shaft, etc are much weaker, I remember when I had my first V8 T-5 rebuilt by D&D and I asked Don JR. the same thing, can I use a 4 banger trans, and he laughs saying sure! for about 2 days, he said they purposely put one in a mildly modified 5.0 and street beat it as you and I would, and it lasted less than 50 hours.
Don't even think about doing this, it just plain won't work out.
Why do you think there are two different transmissions?
Good luck!!!!!!!!!!!!!!!!!!!!!!