Given Fords history on this issue over the last 2 years and my experience with it on my '11...I would be very very hesitant to let Ford reprogram the ECU...it will cause you headaches. Wish I would have never let Ford try and take care of it...because not only did it make the truck a POS in stock form...it did not play well with aftermarket either. Go straight to aftermarket parts such as intercooler, catch can, tune, and performance spark plugs. My truck is finally starting to come together.
For those that are OK with the risk...good luck
2011 F150 Ecoboost Crew Cab FX4, black, 6.5 ft box, max tow, Luxury Package, Bilstein 5100's, Duratracs, SSi custom tuned, aFe intercooler, 170 thermostat