I'd start by checking the ABC's ie Alternator? Battery? Connections? Disconected wires? Error from previous service work? Fuel system (fuel level/pressure/filter/pump)? Grounds (ecu related)? Has the timing been checked? Ignition components good? Just started this or been slowly deteriorating? Knocking noises with problem? Loose timing belt? Mainly happen cold, hot or both? No airflow (air filter)? Oil level good? Poorly maintained? Quick changes in idle or power? Rode hard and put away wet? Sometimes it happens and sometimes it dont? Timing belt old? Unmodified or modified? Violent shaking and shudder? Water pump bearing good? Xamine these again and re-check if in doubt, Y do I say this because these problems you describe generally occur with Zero or poor service.

Your problem is probably buried somewhere in the basics. If the basics are OK, than suspect ECU issues. The Check light coming on may not indicate a problem with the ECU or sensor, but rather may be detecting an improper running condition with the vehicle and is saying SERVICE ME!!!!!

Reprint permission requested on my ABC's thing there. Hope it helps??

Good luck, work safely.

Ozarks Honda Specialist is dedicated to being the very best.