Agreed a blinking CEL is a misfire. Wonder if an injector stuck? I don't see this being a factory tune issue. I could see it being related to a tune though. For those that work at Ford can you see if the car has been tuned?
There is a counter that goes up every time the pcm gets tuned. From the factory this number is 1. It can't be reset even by the ford so if that number is anything but 1 it's been tuned.