I think you might want to look at your main injection timing. It is way too low in the lower end. IMO there is no reason for negative timing at all. I bet this truck is a smokey mess at low throttle and can definitely see why there is no low end power. I'm far from an expert so I'm not trying to be rude or anything this just stands out to me the most.
Also I would fix your throttle "position to desired fuel" F0505 and F0508 just make them linear across the board. For your injectors you might have too much pilot as well and I would advance the timing of the pilot about 2 degrees across the board.
I have attached one of my tunes I made for my buddys 06 5.9 its bone stock just as a comparison I think it can help you see what I'm getting at. Look at my timing calculator vs yours.