So it turns out my intake runner flaps in the B9 manifold was actually touching the cylinder head and couldn't operate at all, and that was why it was throwing the code
The potentiometer voltage is just as I mentioned different from the B8 manifold but it seems the ECU can compensate for this, so no need for any scaling. But this means I have been running the car with fully closed flaps all the time
I have also tried to tweak the thermostat a bit to try to get it to open just a bit earlier with then intention to have better margin for knock.
Right now its running around 96degC instead of 98-99degC as before.
I did a quick log to try to understand the throttle lag when rolling to an intersection and getting back on the throttle. The only thing I notice in the log is a delay of around 1s between accelerator pedal and TB angle. Have anybody tried to improve on this with the auto or DSG trans?
Cheers!