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If your 2000 Yamaha V Star 650 is not getting spark, there could be several potential causes. Here are a few things you can check:
Ignition coils: While you mentioned that the coils are getting hot, it's possible that they are not functioning properly and need to be replaced. You can check the resistance of the coils with a multimeter to ensure that they are within the manufacturer's specifications.
Spark plugs: Make sure that the spark plugs are clean and properly gapped. If they are worn or fouled, they may need to be replaced.
Ignition switch: Check to make sure that the ignition switch is working properly and is providing power to the ignition system. You can use a multimeter to test the continuity of the switch.
CDI unit: The CDI (Capacitor Discharge Ignition) unit controls the ignition system and can be a common source of problems if it fails. You may want to check the CDI unit to make sure that it is functioning properly.
Wiring: Check all wiring connections to ensure that they are secure and free from corrosion. If any wires are damaged, they may need to be repaired or replaced.
It's also worth noting that while the starter motor may be working properly, it does not necessarily mean that the ignition system is functioning correctly. If you are unable to diagnose and repair the issue yourself, it may be best to take the bike to a qualified mechanic who can help you diagnose and fix the problem.
I would call the dealer and have them check the part numbers. If the part numbers match then yes you can. Alot of the time the only difference is the connector. Yamaha has alot of interchangeable parts but the safest way is to verify the part numbers. If you just " try it " and they don't match you just may have fried the cdi box and you'll be trying to troubleshoot a bad part that you think is bad.
CDI stands for "Capacitor Discharge Ignition" It is a solid state system that replaces the old points ignition system. It consists of a control unit, (usually an alloy box under one of the side covers or seat,) and the pick-up or sensor on the end of the crank or camshaft....
follow the plug wire back to the coil and see if there are any breaks, if not might switch coil with the other one and see if the other plug now misfires, if so replace the coil, most cdi problems are not intermittent, typically they either work, or they dont.
could be the regulator/rectifier is frying the system?
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