Something that everyone should know about their factory warranties is that just because your car is modified doesn't mean that your warranty is automatically voided.
The law states that for a manufacturer to cancel warranty coverage they have to prove that the aftermarket modification caused the failure of the part that is under warranty.
There are certain known failure patterns on Mustangs that cannot be caused by modifications(alternators,COP's,sensors,etc).
If your car has,say, underdrive pulley's,CAI, rear gears, etc and the car develops a misfire from a bad COP, then they must cover the COP under warranty(assuming that you didn't damage it).
This is called the Magnuson-Moss warranty act and is designed to protect the consumer.
I work for a dealer and I don't care about modifications generally, however some dealers and tech's are not so generous. They may refuse to work on a modified car-which is their right- but that does not mean that your warranty is void.You may have to search around for a place that will work on it.Do not let them bully you into thinking that they will cancel your warranty.You have legal rights.