You really expected them to warranty the repairs on your car with all the mods you have and not have them deny it because of it?
Even if you could successfully argue with them about the relay they would probably figure some other way around it. With so many changes due to the blower and related mods they have so many things they could claim to be contributing to most any mechanical issue you have on your car.
You can hire a lawyer and take them to court but it'll cost you big $$$, and Ford has lots more money than you do.
If my car had all the mods yours does I wouldn't ever take it back to the dealer for any service.
And FoolnYa, do you already have 60K on your car??? You know the powertrain warranty is 5/60, base warranty is 3/36.