If you have a manual look up ignition coil solenoids. My FJ1100 had the same problem. Take off the small cover on the Left side that has Yamaha engraved on it. After taking it off you will see a metal T that spins around. This metal T passes 2 solenoids. Looking straight at the ignition coil, the left solenoid sends spark to the left side (cylinders 1,3 I think), and the right solenoid sends spark to cylinders 2,4 I think. If you look closely at the metal T when turning the bike over you'll see it passes each of the solenoids pretty much coming in contact with them as it turns. Your problem is that the metal T isn't connecting with the solenoids. Either get new solenoids or whole ignition coil, shouldn't be more than 50 bucks. Then read your manual on how to set the ignition timing. Hope this helps
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