You've gotta be careful doing that. If the minimum airflow is messed up because of an incorrect scalar, the throttle plate actually closes as the vehicle starts to move even though you're comanding it to open more with your right foot...makes it super annoying to drive a stick car with an aggressive clutch. Really need to do what Ed said, dial airflow in with the stock TB and scalar, then swap to the other TB and adjust the scalar. Essentially the PCM only uses the minimum airflow number to determine what a throttle position should be based on the scalar and some math, it's not actually moving the plate based on MAF or SD airflow data...although that's what we use to tune the table when the scalar is stock (correct for the TB on the engine).
I spent weeks banging my head against the wall with my NW102, then I read Ed's post in this thread about adjusting the scalar...so I coped my final airflow min table from my last tune that had the stock 90mm in, tweaked the scalar more, and now the car is a dream to drive...do you have good numbers from the original 90mm? If not, even though this sounds annoying, I'd swap it back on, and swap in all it's stock settings again...then do this procedure with the stock 90
http://www.hptuners.com/forum/showth...103#post136103 then swap the 102 back on, and do what Ed said...if that still doesn't work, then I think you have a problem with the TB itself.
For what it's worth, my scalar on my NW102 on my LS3 wound up somewhere around 6300, not the 7000+ that I originally thought it needed to be.