what are the Map sensor values doing? how about the ect values? and IAT?
This may sound stupid but maybe an airflow problem where it’s thinking it’s starving or have to much? Just throwing it out there.
At what engine temp is this happening at? How are your thermostats? When my truck is warming up and I have the a/c running my truck will cycle the vanes back and forth for a while untill it get past a certain engine temp.
The only thing that seems like it wasn't addressed yet is the hydraulic system of the vvt. You said you rebuilt the turbo. Did you do anything with the solenoid or the actuator seals while it was apart? It's unusual that it completes the test when cold but not when warm, normally that would be reversed, but I suppose that if there was a hydraulic leak that is only presenting when warmed up, this may happen
I'm assuming you've already tried a full flash to a "stock" tune?