how come? i know the newer 4r70w swap from a 98+ 3.8 liter is a very popular swap. and mechanically its pretty much a direct drop in. the only real modifications would be dont electrically because the newer trans have a few different electrical components in them. i dont see why it wouldn't work but i also think i may have remember something about the 94-95 v6 trannies may be weaker than the 5.0 tans. i dont know for sure because all the write ups that i have researched have just said for the best bang for your buck strenth it needs to be a 98-2004 trans and be careful about trans that are newer than 02 not having the splines on the tailshaft for the speedo gear. but if you were just getting it back on the road for a temporary fix i dont see why the 94 v6 tranny wouldnt work. check out clickclickracing.com for some info on what auto trans can be swapped around.
i've been reading up on the matter off and on for the last few years not and have settled for a 03 4r70w out of a v6 mustang that i made sure had the speedo splines, i havent decided if i'm going cheap and doing the J-mod myself yet and convert it over to our style wiring harness or if i'm just going to go with a manual valve body and not have to worry about the electrical in it.
Like I said, the 5-speed bell housings are different. Same bolt pattern, but they use a different flywheel so the starter position is slightly off. The T-5 transmission will work just fine with a 5.0L bell housing.
I don't know anything about autos, but now that you mention it I do recall the v-6 4r70 being a popular swap into our cars. I don't know the details on the swap though.
When I did the 3.8 to 5.0 swap in my 95, the guys at MPS Auto Salvage said that the auto trans would not work and that the 5-speed would work with the 5.0 bellhousin. I am not certain what the differences are. These guys seem very experienced in these swaps so you may want to contact them and find out