One question. You said it will run 16.2 in 1/4 on performance tune, but not on stock tune. I'd say that it isn't an issue with all that stuff that's been changed, but perhaps something with your stock programming.

After all, if it runs fine on the canned tunes, but not stock; everything else with the vehicle is still the same, just not the commands and criteria the ECM is reading and adjusting. This may not be a physical issue with parts, but something else.

BTW, if the dealerships have been in there several times, double check some of the bolts and electrical connectors, looking primarily at grounds, just in case one was missed or is loose.