This just gets more confusing, so may I be forgiven for suggesting a 'long-shot' possibility?
You posted that the anti shudder valve stopped working when you disconnected the vnt pipe. If they have been incorrectly plumbed in parallel the valve would work normally at key-off but would vary it's position according to the vnt demand when driving. Your plots of map seem to discount this since the pressure did not fall below atmospheric on over-run. Also you checked it! However the position the valve takes up may be a balance between spring pressure, vacuum applied, air flow effects and bearing friction. So, manifold hot, more bearing clearance, valve closes further. Cold manifold, after idling, more bearing friction, valve closes less; less drag. Or: high revs, high airflow, valve closes when vnt does, idle revs, low airflow, valve remains open. How this ties in with ecu resets I don't know, but a finger on the anti shudder valve control capsule while revving the engine a few times would test it.