I haven't heard of anybody swapping in the 3 valve 4.6L into a 96-04 Mustang. But plenty of people swap in the 4 valve 4.6L, in fact it's so common that there are companies that make kits with the necessary parts for the install. I would go with the 4 valve if I were you. You can even use your stock ECU with a 4 valve swap, you just need a custom tune for it.
I don't see why not. It should bolt in pretty easily. You will need the engine computer and possibly a few other items from the 3V engine and you should know that your transmission is probably a good bit weaker than the one in the 3V engine cars.