Graphing out your data sets reveals the following:

VGT Commanded & Actual are spot on across the board (Commanded is behind Actual, only a small edge is visible of it)

Boost pressure is consistent with VGT position, RPM, and Commanded acceleration; aside from the fact that you're producing too much boost.

However, Commanded Accelerator Position & Actual Accelerator Position are wildly off from each other for the given time frames.

They may be part of the reason you are experiencing issues.

gauges.jpg