Find a good dealer and stick with them. I got SCREWED by my dealer. I put on a MAC cat back and it worked great, sounded nice. Then my check engine light came on so i took it to the dealer to get it looked at. I was told that they couldn't do anything for me since I had modded the car. I argued with them that, by law, that doesn't void my warranty - only my warranty of that part or other affected parts as jstreet0204 correctly stated.
After 2 hours of arguing with the parts manager and then the service manager, I was told that the check engine light was just a smog light and it was labeled 'check engine soon' because if it was labeled 'smog light' no one would ever take their car in over it. They said that, since I had modded my exhaust, that they couldn't do anything about the light. I should have known better than to believe their line of BS but I did.
So, I left the light on for 2 years figuring that it was just a smog light that would stay on since i later put a catted X on my car. When i started hearing the knocking in my engine, my warranty was done so I took it to a real mechanic (3 different ones actually). I found out from all 3 that the light was on because i had a bad coil on the 8th cylinder and the knocking was coming from inside the cylinder, probably a blown wrist pin but there's no way to know for sure unless we rip apart the whole motor. I don't know if a bad coil can blow a wrist pin but it's a hell of a coincidence. Right?
Anyway, to make a long story short, it was cheaper to put in a new, forged motor than to rebuild the stock motor. So, from my perspective, 7k in the hole, let me tell you that it's a good idea to find an honest, mod-friendly dealer.
Oh, and if anyone wants to know which Ford dealer screwed me, just ask. I'm HAPPY to chase their business away.