c49 pair control solenoid valve
Look around the back of airbox, top of valve cover area for a black or white plug.
Check the connections, and that all the pins are completely seated.
Years back I flashed the ecu on a friend's gen2. He had said he wanted the PAIR turned off. I told him to do the marble mod/block the emmisions hose to the airbox first, and he said he would.
When I flashed the ecu, the bike ran rough, missed and popped, and not the typical pops on deceleration.
When I asked if he had done the marble mod like he said he would, he had forgotten.
So a disabled PAIR Can cause your problem.
It may not be, but given the circumstances, it looks like a good starting point.
And props to Yellow09 for digging up the code