05 ISX 565 Surge, loss of power, ideas?

[tree98]

You have a BAD DELETE!! STOP DRIVING IT IMMEDIATELY!! 45 pounds of boost is gonna crack a piston or the head or both. Your gonna need to pull a copy of that program out and send it to Rawze for review.
Do I understand you correctly that you no longer have the VG turbo on the truck? If that's the case Your gonna need to start sourcing parts to put it back on.
What about the EGR cooler, has that been removed as well? If so your gonna need one of those too. Without it you don't get proper cooling to #5 & #6 cylinder's . It's also hell on the water pump.
These engines can be demandated correctly and live a long productive life, but there are certain rules that must be followed, that's just how it is with Cummins ISX engines.
Atleast you stumbled onto this site. This is literally the only place on the planet to get all the best and current information regarding ISX engines, welcome aboard.