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I would take the JBA mufflers to a muffler shop first and see if they are the problem. Ford dealers are less then receptive with the after market mufflers.
You will probably need to use a relflasher like a Diablo predator. Anything involving the air intake or exaust on the 05's+ can make them act a little funky. Regardless if one works and the other one doesn't to get max potential out of your bolt ons you are going to have to reprogram the computer.