Low trans fluid levels can cause all kinds of weird issues. As can a faulty ptu. and you won't have codes to help you either. checking the fluid level and condition in both cases, plus any signs of leaks at the axles etc should help eliminate some strong possibilities.
Would also check for chafing knock sensor wiring. Has reared its' head across gen 4 & 5, tho mostly gen 4.
Pulling the plugs gives you a quick honest eval of engine health of course.
What fuel are you running? Any changes in stations?
Doesn't sound like intercooler buildup being sucked into the intake, since you are in low boost conditions.
Are you stock or tuned? If tuned, return to stock and evaluate.