There is a bit involved. Not to terriable but time consuming. You will need a K-member, I would get ALL the harness's from a 94-95 gt from a junk yard (engine, Tranny, Computer, cluster, and engine fusebox etc..., I would also probably change out the cluster since everything is electronic on the 99+ with an 94-95 Mustang Gt/cobra cluster (You can wire in all the stuff to work with the 99 cluster...just depends on the time you want to spend and it might end up getting a shy costly with buying little things here and there).
Just note that you will still have to do some hard wiring too probably to help convert stuff over.
You can run an 94-95 GT Computer and that would work good. But I would try to running an A9L. Better computer for performance/tunning etc..
On the Tranny (the 4r70w from a 4.6 wont work. Now you should be able to get a 4r70w from a 1996 Ford Explore and of course use one off an 94-95GT.) I would use an AOD though if it was me. You can convert it to a manul valve body (Cheaper LOL). (IF you were wanting to do that lol). You will also need to get a Drive shaft for/from a 94-95. The balance will be off if you use an mod motor one.
The brakes dont worry about. I would use the hydro boost that is stock on the 99 Mustang, and the
suspension you wont have to worry about either.
You should be able to go to a junk yard are a pull a part place and get mostly everything you need and help save a lot of money. Like I said I dont think its too terriable but it will be time consuming.
Hope that helped a little