it sounds like your torque converter to me, I didn't have exactly this problem , but I have hda that happen to me before, upon asking the "ford certified transmission specialist" at my local dealer, he explained that it was a "lockup" and that its perfectly normal and nothing to worry about.
If you didn't reset your computer that may be why its doing it. Or, if you started off after a fresh reset driving it hard, it may have adapted in a strange way.
I would try resetting the computer again, this time idle it for 10-15 minutes and then baby it for a short drive and turn it off, then whenever you go somewhere drive it easy for probablly 2 oe 3 days, then it should be ready to play.
if that doesn't fix it, and you have the time/money for a shop to look it over, you may want to take it down somewhere and drive em around, see what they think.
IMO ford wont be able to help, chances are thye'd blame it on the filter 100%, they've given me a hard time about mine a few times, but never taken any action. (probablly cos they're legally prohibitted to take any

)