Find out the name of Ford's Regional Service Rep(this guy works for corporate not the dealer).
Then set up an appointment to see the general manager of the dealership. I would let him know what is going on and let him know that you aren't about to bend over and take it. Tell him that you thought you would try to get his help before you contacted the dealerships principal owner. If the general manager won't help you ask for a meeting with the principal owner. If the owner won't help you let him know that you are going to work your way up the food chain until you get your car fixed under warranty. Then you need to contact the regional who despite what he may tell you has the authority to bend the rules to take of special situations.
I am sure they wouldn't want one of the Mustang mags to publish your story on how the new Coyote engine is a POS and how Ford won't honor their warranty claims.