Correct. Don't forget to replace the trans cooler on the frame rail at the same time. (one thing i havent tried yet but would love to experiment is the TC from a current High Output truck. I hear that is the main difference in the power rating.)
i had a similar problem on a six oh excursion and it was tune related. switched tuners and it went away. (i see you have swapped the pcm so probably no help)
Try reseating the plugs on the drivers side inner fender.
Also could disconnect the alternator charge wire to eliminate a wacky regulator. It will have a battery light on of course but should run off battery voltage for a bit anyway.
dont delip the maxxfoce pistons. Idle haze and poor cold weather charactaristics arent worth it. Running a close to stock setup you wont crack one anyway. Just get good tuning that keeps the spray in the bowl.