Actually the 99-04 GT calipers are a great upgrade because the dual Pistons spread the calipers force over a greater pad area. You get more bite.
Rotor diameter does help with braking power, but it also helps cool the brakes in a road racing application due to more mass.
Basically, cobra 13" brakes great for road racing, GT 2-piston brakes great for drag racing as smaller diameter rotor takes less power to spin. The calipers will offer good bite in a single hard stop.
Both caliper swaps require a MC change as well. When using the 99-04 2piston GT calipers, you will want to run a 1993 cobra 1" bore MC. It's a direct swap onto 94-95 GTs
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