Logan said:
The bottom line is this, as verifiable by the Magnusson Moss Act. In order for Ford to void your warranty, they must prove that the modification made is the direct or causal factor in the warranty claim.
Unfortunately, this isn't always how it works. I just wrote something about this, so I'll copy my text about warranty claims.
Maintenance example:
My parents lost a warranty claim with Ford in 1991 because the dealer basically said the engine failure in their wagon was based on lack of proper maintenance, thereby voiding the warranty. Once the dealership made their decision & explained themselves in writing, the ball was in my parents' court as to whether or not they should hire a lawyer & pursue legal action. They consulted with one & he told them it was probably gonna take a while to go to court & then it wasn't a sure win, so they ended up buying a new motor & the dealership installed it at a reduced rate.
Another example:
A Bullitt owner at BullittClub has documented his problems with Ford - he had a chip installed & after numerous problems several months later, the car went in for extensive service. When the heads were pulled, the cylinders on the pass side were scorched & a couple pistons were actually cracked. The dealer said the chip leaned out the fuel & basically burned up the chambers. The chip manufacturer said no way his chip caused a lean fuel condition & so the owner was stuck in the middle. But at no time did Ford ever prove that's what actually happened. He maintains his car was always exhibiting the problems he was having; they just got worse after some of the mods.
And my last example is personal:
The new Tremec 3650 in the GT's & Bullitt's grinds the 1-2 shift; as a result many of them go back to get a new shift fork (mine included). When I took mine in, I was asked if I had installed a new shifter & when I asked why that mattered I was told "It might contribute to the problem." Talking to the technician when I picked the car up later that week, I mentioned I was going to install a Steeda Tri-Ax & he said it was smart that I had waited because the Service Manager probably would've voided the repair, even though there was a TSB issued specifically for that problem. When I asked how they could prove that, he said they usually just say it was installed improperly, because they don't want to get in a pissing contest with the aftermarket manufacturer by saying it's a defective product. Since then, I've gotten in writing that my Ford gears won't void any drivetrain warranty, when installed by a Ford dealership with Ford fluids. So there are certainly dealers out there who will work with you on mods & you can get things in writing if you want to, but I wouldn't just assume the dealership is gonna be an advocate for you if you need warranty work done. So that's my nickel.