Dave,
I've spent the past 1 1/2 year modifying my wife's 99 GT convertible. I dynoed it stock and after some mods. I'm almost done with the mods and will head to the dyno and the track soon to see what kind of bang I got for my bucks. Assuming that you know how expensive it is to go fast, I'll list the mods in order most bang for the least bucks.
3:73 gears (you'll also need a correction box for the Speedometer)
70 mm throttle body
Supercharger (or other power adder Turbo, juice etc)
Headers and x pipe
I put exhaust last because the 99 up GT's have pretty good heads and exhaust. I spent a lot of money on headers and a complete Bassani system (X pipe etc) and got 12 horsepower on the dyno. That tells me Ford did a good job on the factory design. The exhaust upgrades really pay benefits if you plan to supercharge it
Bob