I have 2006 5.9 with Goerend parts built tranny(less than 3K miles on build), Jacobs exhaust brake, with stock turbo and no internal engine changes. Parts include Valve Body, Servo spring, Billet torque converter 900/400, GT1 rebuild kit, GM governor solenoid, billet input shaft, Billet flex plate, over sized pan. I have a Smarty Jr on tow mode. Truck has 28000 miles mainly used towing 12K 5th wheel.

Last towing trip with fifth wheel from 5K feet to 10k feet last Fall no issues.

I recently noticed driving to and from work that when I floor it to accelerate onto interstate, tranny downshifts then engine struggles with not much increase in speed, RPMs slowly increase, tranny temp stable, boost goes from 4psi to 26-28psi instantly, and EGT goes from 600 to 1200 instantly.
When driving normally the shifts are firm and no spike of boost or EGT.

I am going to return truck to stock programming tomorrow and see if that helps.

Any ideas?