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No, especially if you are using the GT500 brake upgrade kit or parts. I did it to my 2007 Shelby and had no problems. Stopping power was a huge improvement.
The GT500 booster is supposed to offer more pedal assist. I went from stock 11.5" V6 rotors to 14" brembo's and 13.8 rear rotors with the standard v6/gt booster. Pedal feels fine.