Have you tried running the bike without the o2 sensor hooked up? Totally unplugged, no resistor, no o2 optimizer.
The controller is supposed to 'trend' to 13.6 AFR with the o2 optimizer plugged into the loop with the o2 sensor and PCV.
If your map is like mine was, the area in the yellow in the attachment above adjusted, then having your 02 sensor plugged into the mix may be causing some of the issues.
We were seeing that on the dyno when he was trying to adjust the fuel on the cruise circuit, he'd make a fuel cell change and the bike would adjust for it. Until he moved the numbers way out of range, then the bike would hiccup and run lean or rich depending on the fuel adjustment. Mine has the supplied o2 optimizer plugged in.
I'm going to try the map from dynojet and if that doesn't help, I'll unplug the o2 sensor and run the map that was done on the dyno. Problem is, that map is probably not 100% accurate because the adjustments were made with the optimizer working in the loop.
PM me your email if you want to try my map, I would like to try yours.