Tell him not to sweat it....some dealerships are ********* about warranty work, and for that very reason, there are only two in my general region I would even take my truck or Shelby to for warranty work. One in articular wont warranty a ****** TSB recall from Ford for Christ' sake.
You tell him if the service rep gives him any ********, ask for the service manager straight away. Tell him not to loose his cool with the service manager, but be forward, direct and stern and tell the manager the following. " I have abided by the terms of the Ford Factory Warranty, and have not used this vehicle for anything not intended. This vehicle has been properly maintained, and not modified in any way that would breach such warranty. If you choose to not cover this issue under the warranty, I will first call the regional Ford manager and report this act to him, and my next call will be to my attorney to file suit for non-performance under the contractual obligations outlined in the warranty, and while I am fully aware of the arbitration clause which allows Ford Motor Company to choose the venue, my legal team will tie up every employee in your dealership that so much as laid eyes on the vehicle with exhaustive discovery interviews and mountains of paperwork." If he hard balls with a response that they have ample proof that it was neglect or abuse, remind him that the burden of proof to severe the warranty is completely on him, and the proof has to be undeniable. Then remind him that you are very active on the Raptor, SVTOA, F-150 forums, and you will make sure that this issue is spread across every single one of those sites, and then tell him to discuss such an important decision with the GM and owner before he makes any response to you. Tell him you expect an answer in the next 24 hours and say goodbye and disconnect.
If at that point they refuse, there is probably something we arent being told about what was done with the truck. However, calling the regional ford rep would probably be the only option unless you do try a legal option.
That and getting rid of pesky phone salesmen are about all my lawschoolin' has come in handy for....but I write a mean legal action letter from time to time....usually works....good luck.