A couple of things to consider in this;
1. Warranties and performance expectations are based on the manufacturer's stock configuration. That said, Every manufacturer makes a bad one sometimes.
2. The "Lemon Laws" in every state are different. What goes in Colorado is not the same as anywhere else.
3. It's the dealer's responsibility to diagnose the problem or problems and identify the failure cause. The dealer is expected to use his best judgement to make a fair and accurate decision. If the owner does not agree with the outcome he/she has the right to pursue legal recourse under the M/M warranty act.
4. When ever we modify a vehicle we possibly void a part or all of our warranty. However, not all mods affect warranties.
5. Sometimes things just go bad and there's nothing we can do about it.
My advice; take it to the dealer. You pay for your mistakes, Ford pays for theirs.