OK, this is the story.
Back when the LLY came out, and people started putting on either aftermarket aircleaners, EGR blockers, or exhaust systems, AND they went driving in the mountains, the infamous P0299 Underboost code came up. It is a performance limiting code, so it was important to resolve. It was often accompanied by MAF codes.
What was happening, is that since you altered the air flow going in and out of the engine, the MAF sensor reading + the baro sensor reading, did not line up with the boost sensor reading. So the GM computer "guesses" at what is wrong, and it figured there was a problem with the boost. The boost sensor itself still was reading OK, the turbo was fine, but the MAF reading was different we found.
So it is unlikely that there is really anything wrong with your truck UNLESS you are bone stock.
The easy fix is to increase the boost error limits to 15 psi, IIRC, as Othergirl posted above. Trying to "recurve" expected boost is fine, editing the MAF sensor scaling, etc, will all git-er-dun but the boost error limit is the most reliable way of killing it.