I peruse this board on a pretty regular basis but oddly, had never checked in on this thread... get this one fellas.. I have a 2010 Expy Ltd, that is at my local dealer as we speak getting the hood and tailgate repainted. While in, I am having them fill the goofy-a** holes from the Expedition badge and leaving all of the badges off.
Here's my abbreviated story... I get my car washed at minimum 1/wk, detailed probably 1/quarter. A couple weeks ago, I noticed the bubbling on my tailgate, under door handle. Took it to the smaller of two dealerships near me to show him, telling him I knew it was a known issue with the last generation, but thought they had had it resolved. He came back at me with "yep, it's not prepped right from the factory, happens all the time, and proceeded to tell me the hood is usually first, and gets worst."
My car has just about 32k on her already (I too drive alot) and he was actually pushing me to get it in and fixed. The fact that some are out of the 3/36 warranty could be of concern, but someone above suggested, call FoMoCo, they WILL at minimum meet you 1/2 way or better to make you right. I know this too from first hand experience with 4 different Ford E350's and 250's with the lock tumblers in ALL of those vans, they were pretty darn good to me.
That wasn't exactly abbreviated, sorry. But good luck, be cool with them, yet firm, you will get it fixed.