Screw on throttle body is for setting BASE IDLE, the CO trim as said is indeed on ECM, even at stage 2 it will if all ok fly through test on emmisions with no adjustment needed at all.
The fuel mixtyre is not set for the stage 2 chip, the settings for fueeling are contained in the map on the stage 2 chip in the ECM.
The idle trim is seperate and not controlled by chip but has a very minute amount of influence over overall load fuelling.
The co needs to be around 2-2.5% to work best, which will easily pass the test of emmisions as is well below limit.
tabetha