I have dealt with the same coding issue that you described for the past six years. I worked with Brian and also with Mike. I did several tuning cycles with the ECO Tune. The backstory is that I had the first Cosworth supercharger installed in the US purchased through Brian. Then several engines in Europe exploded with too much boost.
Cosworth offered to rebuild my engine for free with new pistons, rods, etc. I sent the longblock to them in California and they rebuilt it. My mechanic here reinstalled the engine, which is when my problems began. I also have the same exhaust system you describe, but also a catback muffler with dual exhaust.
Last year the same mechanic finally figured out (after I had replaced multiple parts, including the throttle body and O2 sensors) that the electrical harness had been crimped by the cosworth supercharger and was shorting. It cost $1,400 to buy the last avalable electrical harness and more to have it installed. I now get a couple of codes about once every 2-3 weeks, but it runs smoothly. Before, it would stall when idling or even when driving. Don't know what more I can do to completely rid the codes. I sent my data recorder file to Mike after the intall of the new wiring harnesss and he confirmed the the tune is good.
It has been really frustrating, but I do like the boost.