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My experience is that the stock setup with upgraded pads and and fluid is just fine for continuous 120mph-40mph hard braking on a very technical track during thirty-minute sessions. (Pad suggestion thanks to Mr. Dave Zeckhausen)
One other possible contribution to this is that, perhaps, the OP didn't have enough pad-thickness for the additional braking that was needed as a result of the addition of the supercharger (higher speed = harder braking). Brake pads serve as both a friction surface as well as heat insulator between the disc and the caliper. Not enough insulator means more heat entering the system.
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