The Magnuson Moss act was put in place to keep dealers from denying warranty on non OEM parts like fuel filters and spark plugs. It was never intended to help someone when they installed performance parts. I'll say it again it will be up to you to take the dealer or car manufacturer to court. And they have a lot more money to fight you on it.
Incorrect. The Act covers warranties on repair or replacement parts in consumer products, there is no distinction for OEM and non OEM.
Law aside, it is always in the best interest of the dealer to cover warranty items. Primarily it is the good will to their customers, but secondary, Ford does pay them for the work and it is an opportunity to sell more work to the customer. If the modification clearly did not lead to the failure, Ford WILL cover it. The dealer does NOT want to go to court any more than you. The consumer also has the advantage of the office of consumer liaison that every manufacturer has in house to advocate for them.
Mod away, just be aware if your mod leads directly to another failure it may not be covered. other than that is is required by law to be covered.