Headers, exhaust, gears, intakes, throttle bodies, a tune that allows the cars to run within Ford's factory parameters, and basic suspension mods are not a problem. This came from Andy Mohr's service manager and Pearson Ford's service manager. Keep in mind this was with Ford installing the parts.
Pearson Ford is installing all the stuff I have bought. The service manager seems pretty cool about mods. He said that if the non FRPP installed part causes some sort of damage and it is directly related to the failure, the warranty covering that part and any other related damage is not covered. If the failure is not directly related to the failure, no warranty issues.
I understand some service managers are understanding and will take care of most issues, but when you blow a motor, isn't it fords decision whether or not to warranty it ?