I'm a little late on updating this one. In the end the ECM was not the issue nor the programming. The reman turbocharger was causing the issue mechanically. I had the rebuilder go through the turbo but they could not identify the fault. A new Holset turbocharger fixed the issue and the truck is running normal again.
Looking back at this one, I think I overlooked the high current draw from the actuator. Since I could not confirm if the actuator was fight to stay in the closed position or if it was trying to open the VGT. Going over my old captures, I did find a truck that had a turbo stuck in the closed position and the waveform looked just like this current one.
Thank you for the update and there's always something to learn!
Great to have some closure on this one and it will be good to revisit the files again. Did you manage to get a known good or a confirmation of the fix with the new Holset turbo?