My 2003 R1 with PC III is doing something weird when I wind it out and shift to third. From a stop, hit it at full throttle and hold it wide open to 11,000 rpm and shift. Continue to hold full throttle and right before 11,000 rpm in second gear it feels like the chain skips a tooth, or the ignition cuts-out for a split second, like on a quick-shifter. Kim says it blows a puff of black smoke when it does this.
My memory is for shit these days, but it seems like it has done this before and it went away.
Any ideas? I guess I should disconnect the Power Commander and see if it still does it. I don't think it is the PC, though, as it only controls the injectors and not the ignition.