The Split-Port engines will require a bit of modification to work. For one, you'll need to modify the harness for the injectors and get a modified fuel rail. There's more work, but I don't know what ALL else is involved. Do a search on 3.8mustang.com or V6power.net about the Split Port swap.
The Single-Port engine will plug right in. I helped my friend put a '98 engine in his '94, and we had it running in no time.
You may notice in searching that a lot of people have problem with the split-port swap. I have another friend that has a '96 ex-V6 with a 2000 GT drivetrain. He tried a split port on the car when it had the V6, and couldn't get it to run right so he just dropped in the PI4.6.
It all depends on how much time and skill you have. If this is someone's daily driver, I'd just stick with a '96-'98 engine(stay away from another '94-'95 all together). If you don't need the car for a while and feel that 40hp is worth the challenge, go with the '99-'04.