I doubt this is it, but if your accellerator cable linkage is not allowing the throttle to return all the way, you'll get the APPS error and your truck will go into "limp home mode". I ran my '03 motor through some deep ice and mud (yeah sounds redneck) but the truck went into 1000 rpm limp mode, and wuldn't respond. Popped hood and removed lots of ice mud and crud, did a restart and it was fine. If the cable doesn't allow proper movement and it's not in the normal resting position, it'll toss the code and go into limp home mode. The hole was about 3' deep, the motor in an H1, and the run was about 75' of crud. Again, probably not your problem, but worth looking into. I'd clear the code with a scanner, check the throttle body and see if it comes back (if you haven't).
Oh yeah, I have an '06 - I baby it.