I dropped it at the dealer this evening, and should know more tomorrow. That said, I wouldn't worry about it--I'd be really surprised if this was a chronic issue.
Same symptoms on my 2011 SCREW, build date ~15 Nov. Here is what was learned:
1a. I experienced the Tranny going into limp mode, which can be either 3rd or 5th gear operation (Not sure how it decides whether to give you 3rd or 5th). This is a self protective mode that allows you to limp to safety when the PCM believes there is a major powertrain issue.
1b. I had experienced a clunk or 2 when this first happened from the drivetrain.
1c. Recycling the key didn't by itself change things, but by letting it "cool down" the symptoms went away. I think it would fault when the Tranny hit 194 Degrees if I remember correctly.
2. This was a 2011 Raptor that escaped Dearborn with a bad PCM. It took 5 minutes for Ford to tell dealer this was a PCM problem and 15 days to get the part. This was in early Dec. So hopefully the PCMs are more readily available now.
3. Your Dealer, if unaware of the 2011 PCM failure symptoms, might concentrate on the 6R80 (tranny) as the culprit. If you find them wanting to drop the pan, you might encourage them to call Ford about the PCM issue 1st.
3. The BCM issue affected only a small portion of the F-150 line; not likely related to your symptoms. While its in the shop, I would have them physically verify (as opposed to by VIN) that your BCM is not one of the self igniting models.
Hope that info helps, good luck.