We talked to the service guy at the dealership about this. He told us that they had a lot of problems with burned up tranny's due to chips, so when the "big guys" come out from Ford to look at your vehicle if there are any tranny problems, they will not honor the warranty if they see you have or had a chip.
The head service guy told us as that we can do an exhaust, air filter kit and guages and the warranty will be good. If we do a chip and have any MAJOR trouble and the "big guys" find out when they come out to take a look at it, they will NOT honor the warranty.