Was the CEL there before you flashed, or only show up after?
The AP maps specifically say what intakes they're designed for (if any). Using anything other than what they specify can lead to problems, so that could be your issue right there. What exact intake is it?
And yes a bad o2 sensor could certainly cause boost issues. You may have a vacuum leak too. How long has the car been doing it for? Mileage and service history please.