If something seems to be running on 1 cylinder, you usually look into the ignition, or something electrical. Determine what you have for an ignition coil. Test the coil for ohms resistance. You can usually find the specs (for most coils) on line, or in forums. Check your plug wires. Make sure they are not corroded or cut. Make sure they are secure. Determine what you have for an ignition (pick up). Visually inspect it. See if you can find a test procedure for it. Test your charging system. Trace your ignition wires. Make sure that they are all secure and that none are creating a dead short. Inspect your ignition switch and breakers. Make nothing is touching ground in those areas.
Harley Davidson Ignition Coil Test