That sucks man, there is a MM&FF sitting in front of me that has a long in depth article over exactly this situation. It's June 06 if you can get a hold of one it has some tips for dealing with these situations. They talked with several Ford dealers and officials.
It talks about a 3 step process that you can go through if your claim is denied.
"1. Contact you Sales Rep or Service Advisor at your dealer.
2. If your inquiry or concern remains unresolved, contact the Sales Manager, Service Manager, or Customer Relations manager.
3. If you require assistance or clarification on Ford Motor Company policies or procedures, contact Ford Customer Relationship Center at 1-800-392-3673 (FORD)."
"If you are still unhappy, you can persue a Dispute Settlement Board. If it comes to this, it says that you should go to an independant shop and get a certified, experienced mechanic or expert to make a statement saying that the personalized items installed on the car did not contribute to the loss. Then, go back to the dealer and show them what this expert said; tell them you think they should reverse their decision on not honoring your warranty, and that you're aware of the Magnuson-Moss act and their responsibilities under it. But don't be confrontational."
It also says to try taking it to another dealer before you get Ford involved.
It also talks about the FoMoCo - Dealer relationship as being franchisor-franchisee. So did a dealership representative deny the claim or did a Ford Motor Company representative deny it?
Hopefully this is of some help and I didn't type all this for nothing, lol. Just trying to help.