By law, using aftermarket parts will NOT void your warranty. If you need a warranty repair they must do it for you unless it is PROVEN that any modification that was done was the direct cause of the failure.
See Magnussen-Moss Act.
Like many matters of law, it's important to balance the cost of the process with the potential outcomes.
You get yourself into a situation where you and Mr Ford are head-to-head over a matter of fact, you better be well-armed with science, logic, and data.
Much better to resolve any disputes at the before-contest level. Be calm and show your understanding of the position of the service writer, the service manager, the dealership, and Mr Ford. They are going to want to save the corporation as much money as possible, without completely alienating you or any potential future buyers of Ford products.
They are also bound by the same rules you are: beneath it all, you are responsible for your actions (products). If there was a failure due to materials or workmanship, or design, Ford must make it right. If the failure was due to mistreatment or misuse by you, Ford doesn't have to give you the time of day. They will cut you a little slack if they can, but you need to make them want to.
Unreasonable demands or threats won't do you much good. "Prove it" may be the law, but it's not a likely road to satisfaction.
"In this universe there are things
that just don't yield to thinking
—plain or fancy—Dude".
—J. Spicoli, PolyPartyPerson
ADDED: 2014 GT 5.0A conv. black: electronics, comfort, security, CA plate (FLICK U); assembled 06-13-2014, delivered 09-25-2014; odometer today (03-21-2016) 4,321.5(--> DELETED --> 2013 5.06M coupe, black:: Odo LAST day (09-25-2014) 7,975) (--> DELETED --> 2008 GT/CS: Odo LAST day (10-22-2012): 9,719.3; #2075 of 2509 convertibles, #560 of 718 in Ebony. 2009 GT/CS: Odo last day (09-08-2012): 12,000.1; #34 of 1705 coupes, #3 of 377 in Performance White. <-- DELETED <--)