First you can reset all learned values by using Category 1 selection 7 will clear adaptations. Try that bcuase you might not be fueling properly due the air amounts. Are you 100% sure the 02's are in the right place. Turn off the Autoclear Check light codes. If you dont know if you have it on go to screen 1 and use option 4 and get out of the menu as normal when you use the track down button on your steering wheel.
Car idle do the 1/7 clear adaptations let it idle for a little bit. Go to map 4, which is factory boost but allows the JB4 to keep track of codes and such. Drive the car 10 miles, some boost some without. From there go to map 5 and drive again. If your still getting a stumble use the JB4 to figure out what codes. If it throws a code, use the JB4 to figure out what it did and why. If its a missfire use the cable to see what your long term and short term fuel trims are. As well note which cylinder the missfire was on.
Report back when your done.