I think I have done everything I can do at the moment. Idle seems to be smooth around 680rpm MAP is around 67.5 - 70 KPa. Adjusted torque management, thanks @GHuggins I found some very helpful information on this from another thread. Never touched this on GEN4, and still scratching my head if I did this correct on my 5.3l VVT (reverted back to stock for now I was also playing with VVE VVT tuning and must have got something out between CAM degree because I set off a MAP inefficient code around 25mph twice once with torque tune and again after torque tune was reverted back to stock.), but on non VVT this helped out smooth out transition between gears at cruise, tip ins.

I disabled burst knock in hopes of this was the culprit, but this did not do anything, and logs show nothing for burst knock retard before and after. I went on a dangerous limb and disabled knock, and everything was very smooth across the board. This is enabled now as I am looking into a better strategy, but this has to be a muffler bracket or something causing this. Its to random and attach rate varies.

Owner will be installing a CAI after this I will check the tune on the MAF and hope to have a better strategy for the knock control.