Got the advice below on SC vs. Turbo for the 3.8. I have done the math and the turbo is cheaper than trading cars. It comes with new headers, fuel system amd injectors for the price below. Could generate 275-300HP with 3.8. Any comments appreciated.
Generally I think it's a bad idea to start with the V6. If you want performance, trade it for a GT and supercharge that, or just buy an '03 or up Cobra. That said, some still like to tinker and I certainly understand that.
One thing you should consider right off the bat is that you will want to add as much power as possible. The best way to get that is with a turbo kit. Take a look here
http://www.proturbokits.com/fordstreetkits.htm. They only mention up to 2002 also but I bet if you ask them it covered 2003 too. I would avoid all centrifugal kits because they won't give you enough boost where you need it, everywhere. You need big power gains everywhere, not just at redline like the centrifugal blower will give you. I would strongly recommend going straight to a turbo for your car. The kit is $3699 according to their webpage. Looks like a great kit.
Do not get a chip! Exhaust mods compliment any other mods nicely and turbos need free flowing exhaust. I would get just the turbo kit, and perhaps an exhaust upgrade (cat-back). Warranty will be out the window on the entire drivetrain. Generally, the drivetrain and engine can easily handle 50% more power and torque.