All good answers... I have a 92, so I'm partial to the 5.0, but I started out with a Paxton SN-92, which was ball driven. I kept siezing bearings. They finally cam out with a NOVI-series, which kicks butt. Ihad laready bolted on an S-trim Vortech, which IS LOUD, but I like it, since I don't get as many imports pulling up next to me and revving any more.
As for the ATI, the setup is a little time consuming and it does include an intercooler, BUT... every time you have an intercooler, you have to consider that every 90-degree bend in the intercooler, you are going to lose about 1/2-pound of boost! Vortech did meet consumer demand and has an "SQ" series of blowers that stands for "Super Quiet."
Basically it all depends on what you want from your car and being supercharged...
If you want to drive it every day, and keep it somewhat streetable, the Saleen/Eaton/Motorsports blower found on the new 03 Cobras is intercooled and very easy to work with. It's not noisy at idle and fits under the hood and is pretty good for up to 9-lbs. of boost.
If you are looking for anything over 9-lbs. of boost, go with either Paxton or Vortech, as they are now one company, because both of them have been proven to whip up pretty good boost/horsepower numbers on the 4.6 motor.
One thing I would suggest before bolting in blower is upgrading your BRAKES! Get some BAER disc brakes so you can stop your
Stang before adding more power!!!