How many miles on your truck?
When I bought my truck it came with the hypertech programmer, and honestly, after removing the hypertech programming I think I actually gained power. It felt much better in the bottom end. Try going back to the stock programming and let us know if its any better.
Also, just might want to check your mass air sensor. Mine became quite dirty after my K&N FIPK upgrade. The hotwires get dirty, and wont read properly. You can try spraying some electronics cleaner on them, or clean them gently with a q-tip.