Did you figure out what it was? I have an 05 F150 just like yours and I'm having the same issue. Only with mine, the emissions light has only blinked once that I've noticed. But I have the problem of it stalling and seemingly about to die any time it needs to shift down to pull more power. I don't have the choking problem any time I'm over 2000 rpm.
Long way to get around to just seeing if you found out what your problem was...