Update 7-17-09: This post is rather outdated. The car has a substantially different setup. Coilover suspension and a Brembo GT brake system currently.
I found a great deal on a 10th Anniversary Mustang Cobra brake kit so I ordered it. The brakes are much larger than the 11-inch rotors on my 2002 Mustang GT's stock brakes. The Cobra brakes have 13-inch Brembo rotors, much larger calipers as well as stainless steel brake lines that don't expand under pressure. I wasn't too familiar with working on brakes and bleeding the system but luckily my roommates are well established car heads.
Stock Brakes
Cobra Brakes
After a few test stops around the block for leak testing, I took it for a drive in some of the hilly parts of Atlanta. These brakes are amazing. Upgrades down the line will focus on handling and chassis rigidity.