is the issue that your brakes are noisy? ie, you have track pads to give you the braking power you need to match the big hp v8? there may be quieter pads out there, but if you want to upgrade to larger, conventional braking systems, there are the girodisc floating rotors that are larger in diameter and come w spacers for the calipers. gets you more torque on the rotor, more heat handling, also lighter. you can also buy kits to fit 996 turbo 6-pot or (cheaper) cayenne calipers to you car (remember, the 986S uses the same brakes as a 996) for more clamping power and larger rotors; here's one:
http://www.goingsuperfast.com/Porsche-996.html