I would check out the selection of exhaust mufflers at Brenspeed.com. My brother owns a 2000 mustang and has purchased parts from this site and was really impressed with the quality on top of the price.
They actually break out each mustang exhaust package by price, which is nice, depending on what you have to spend.
I'm sure you can find a set of performance headers for it, and performance dual exhaust, I've heard X pipes work good for those cars. Join a Mustang forum, they should be able to tell you more in there.