With my 05, also with a AEM CAI & catless, I used to get the cylinder 2 and cylinder 4 missfire all the time. Almost everytime I went WOT. With a recent Airboy tune, those errors have past though, and I've only had maybe one since the tune. Changing my plugs was on my list to do next.. but with the tune fixing the problem for the time being, I'm procrastinating once again.
So my advice, is if your options 1,2,3 don't work, find a way to get a new tune up...
Also, do you have a knock light? that may be tied into a cylinder on the ECU wiring.