Well that means you have the four speed automatic 4R70W. Ford AOD for all intents and purposes. So that means you CAN put a 4.6 to it.... but you A. Shouldn't until you built the trans a bit, that trans isn't super awesome and B. You need to make sure you get the correct block. They changed the bell housing bolt pattern. I would get a 4.6 out of a 97 Crown Vic, preferably a police interceptor if they had that package because that would most likely give you the high output you're probably going for. While you're at it throw heads and cam on it. It is SOHC Modular though which would pretty much count me out. I wouldn't screw with the SOHC.
My suggestion: either throw a super charger on your 3.8 and build the engine with bottom end stroker type of upgrades and heads and cam. OR! This is what I really suggest! Get a high output 5.0 out of a mustang and put that in there!