Trying to work through tuning a friend's LQ4/4l80e swapped 02 silverado. He is running the stock 5.3 harness that came with the truck (with the correct added wires for the 80e and the swapped wires in the main plug) and using the stock 6.0 ecu from the donor truck which was an 02 as well. Truck is starting to drive better from a trans standpoint at part throttle but will not shift WOT correctly. Tune has the stock shift points as verified against a stock file from the HPT repository. Truck has a 3600 stall from Yank I believe and the Transgo HD-2 kit.

At WOT the truck will shift 1-2 and 2-3 fine but will immediately shift again as soon as the 2-3 shift is done. I am starting to think this is a product of the stall or a possible internal transmission issue as I can't find anyone online on any website that has an issue like that. What should I look into?

I do not have a log handy but here is the tune. Note this tune has torque management removed but flashing to a different file with completely stock trans tables and tq management settings and it still shifts the same.