Yes. This will require a lot of work. It's called a split port swap. Pre-99s are a single port setup and have single port style heads. 99-04s have the split port setup and have split port style heads. In order to use the split port heads you will need to swap over the lower intake and upper intake from a 99-04 as well as make other modifications to make it all work.
Try going to places like
www.3.8mustang.com and
www.v6power.net and searching "Split port swap" to learn more about it and see if it's something you actually want to dive into.
Also,
http://www.supersixmotorsports.com/ offers "powerpaks" as they call it for people wanting to do split port swaps or upgrade they're current spilt port setup. I've never browsed the forums there but I'm sure you can find some more good info there.
