stock 99-04 GT has PBR 2 piston calipers up front and 1 piston Varga calipers rear. rotor sizes i think are 11" front and 10" rear.
i have a 2000 Cobra R 4 piston Brembo front kit. they use the 13", actually 12.9" cobra rotors up front. out back i have a cobra brake kit with Varga 1 piston calipers and 11.65" vented rotors.
'00 Bullitt Mustang: Same brakes as 94-98 Cobras (unique red PBR calipers with running horse up front, same varga caliper in rear painted red.) Rear single piston 38mm Varga Caliper, 11.65" vented rotor
'00 Cobra R: 13.0x1.1" Brembo rotors, Brembo 4 piston calipers. 36x40mm pistons. Rear disc the same as the stock '99+ Cobras
Notes on Parts:
The '94-95 spindles are different from the modular '96+ units. The '94-95 units have a curved steering arm and keep the stock track width on a fox3 car. These are the spindles that most people use on the fox3 cars to keep the stock track width. The '96+ units have a straight steering arm and will increase the track ~8mm per side. The '96+ units will give you even more ackerman steering and allows to run the '00R brake cooling ducts or other brake cooling systems. You may need to run a bumpsteer kit to use the SN95 spindles, especially if your car is lowered!
For the year, the spindles, hubs, rear axles, ebrake cables and rear calipers on the SN95s (94-98 for the rear calipers and axles on the Cobras) are the same on the V6, GT and Cobra. So if you are looking for these parts, you can get the parts from a V6 to save cost. Most wreckers charge more for the GT and Cobra parts, so you can beat them at their own game.
Since the rear calipers are the same between the 94-98 V6, GT and Cobra, how do they work with the larger Cobra brakes? First the cobra has a taller axle to caliper bracket to accommodate the 11.65" rotor. Second to accommodate the thicker rotor, the Cobras use brake pads that are thinner than the V6/GTs. There seems to be 3 different rear brackets between the 94-present Mustangs. Any will work, but if you use the GT/V6 bracket with the thicker cobra rotor, you may need to clearance the inside of the caliper bracket a bit.