I did have the exact same problem with mine (06 v-10) summer of '06. Went on a 7000km trip to Michigan and back, and developed a random miss fire on the return trip home. My truck only had about 20000miles on it at the time. I managed to get it all the way home, and a new set of plugs fixed the problem.
I know for a fact I had bad fuel that caused it in my case.
These 3 Valve spark plugs are very sensative to fouling. Especially when putting any kind of additives in or octane booster or anything like that.
I also have an 05 Mustang (3 Valve Head) Superchargered and heavily modified, and lots of experience with failed 3-v spark plugs. I've seen many guys on the Mustang forum I frequent have similar problems after bad fuel, additives, or octane boosters etc...
Your problem is in all cylinders thats why the random misfire code. A bad coil or boot would/should indicate a cylinder number.

I know from experience that these particular plugs can be bad, even though they look good. Going back a couple of years when the 3 Valve heads first came out I knew of a few cases where guys had new plugs bad right out of the box. Until just recently there has only been 1 manufacturer for them (autolite which makes them for Ford also) as well, which limits your options.

I would question how they "flushed" your tank, and what did they do to clean your injectors. The injector cleaner itself could have fouled up a new set of plugs.