Small Engine Troubleshooting Problems? Ask a Mechanic Now.
The Yanmar has three trigger coils and three ignition coils, Start by swapping one of the ignition coils to see if problem changes places. If it does, you need the new coil. If no difference you have a bad trigger coil or harness to it.
# ***** in the above link above are the trigger coils.
Did you find cylinder problem?