The VNT actuator works off vacuum. This is the opposite of wastegate acuators which work off pressure. At rest there is no vacuum so the spring inside the can is the only force acting on it. Your understanding of it is correct. When it's at rest the vanes are wide open and the rod is longest, when the actuator gets full vacuum the vanes are closed and the rod is shortest. When it's running it's somewhere in between. The car modulates vacuum using the N75 solenoid.
http://www.myturbodiesel.com/1000q_how_to/a4/VNTadjust.htm see here for some videos
Have you checked for camshaft wear? There's an article in the mk5 FAQ for this linked below. It was a problem area on the US 1.9L pumpe duses. Worn camshaft lobes would create a lumpy idle or strange acceleration problems. The misfire symptom seems like it might be caused by this. There's a video of a car with a strongly worn camshaft idling too. See this: http://www.myturbodiesel.com/1000q_how_to/multi/camshaftInspection.htm
http://www.myturbodiesel.com/1000q_how_to/a4/VNTadjust.htm see here for some videos
Have you checked for camshaft wear? There's an article in the mk5 FAQ for this linked below. It was a problem area on the US 1.9L pumpe duses. Worn camshaft lobes would create a lumpy idle or strange acceleration problems. The misfire symptom seems like it might be caused by this. There's a video of a car with a strongly worn camshaft idling too. See this: http://www.myturbodiesel.com/1000q_how_to/multi/camshaftInspection.htm