First, don't expect a lot out of your nice V6 auto. While I think the V6 Mustang is a great car, the performance version is the GT, it will take a lot more money to get your pony as fast as a GT.
Having said that,
Tireburner is right.
Change your rear end gears, I'm not sure on ratios for the 7.5" axles but a 4.11 ratio would be good.
A K&N air filter and cold air kit should be on your list.
You might want to go to a true dual exhaust system, an off road H-pipe (if you have no emissions testing) and a cat back system.
As far as the other bolt ons go like Throttle bodies, pulley's ect. I'm not sure what you'll gain on the 3.8L and what the price and availability is like.
There is a forum for V6 owners on this site, I recommend you visit it.
