I have read almost all replies so please pordon me if I am off base or in left field.
(Just got back from vacation). The warrenty issue has always been an issue with Ford on modified cars. I also was a Tech for a local ford dealer at one time. The thing is this....it's who you know!
Especially your attude that sets the tone when you bring your car in!!!! All it takes is for someone to piss off the service director or manager and he/she will put in a commit in your service file(Flagged). At the begining of my time at the dealer there were 2 hard core race guys that actuallly brought in work off the streets!$$$ The 2nd. shift service dept. made money...almost more then the day shift. It also wasn't a big deal to repair head gaskets on cars with the Nitrous bottle in the trunk still attached!!! I know...I repaired one of them.
The night manager got into a disagreement with the directer and soon we had a new night manager. He had a major hard on for voiding factory warranties!! It was like these guys reminded him of the bullies that stole his lunch money, back in grammer school. That caused a lot of money to be lost due "custmer service" and shortley afterwards the second shift was closed down.
Now in todays day is it possiable that Ford is trying to save some money from every angle because of the economy...maybe... just beware anytime you put parts on your car, it you can void your shyte.
Everytime you go back to the dealership for repairs, clean your car and return it to as stock condition as you possiably can. Also be as nice to the service wrighter...believe it or not it helps a lot!
my 2cents