Jim, reading your posts sounds like the problems I iniatially had, was it the AI, was it the exhausts, was it the mapping, I was really tearing my hair out until I bypassed the 02 sensors.
What was fooling me was I would some times start the bike up in the morning and head up to the highway (about 5 miles) everything would be fine, get on the freeway and ride for about 100 miles with no problem, until I arrived at the next town and had to reduce my speed and go through the gears, thats when it started coughing and sometimes stalling on take off with an iratical idle.
Unbeknowns to me the 02 sensors had gone into closed loop which isn't noticeable you at freeway speeds.
So then I just limited myself to some local rides and it became more apparent that after about 10 miles it always started running like a dog after starting and idling fine.
Once I bypassed the 02 sensors my nightmare was over.
The way it has been explained to me is that regardless of what base map you have in the ECU it will still gather information from its sensors and vary its mapping accordingly (within limits), so initailly the bike runs fine then gets a message from the 02 sensors saying it doesn't like the mixtures (due to AI being removed and a free flowing exhaust)so goes into closed loop, I suspect this could be a cause of a constant engine light appearing.
The only way I know of bypassing the 02 sensors is with the tuneboy program.
Keep us updated on your situation, meanwhile I will try and contact Wayne (tuneboy) and see if he can do a technical write up on ECU's and their workings.
Cheers
Davo