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I charged and replaced the battery, charging system checked at dealer. press the start button and it "clicks" lugs, then most of the time starts. Place a charger onit and it fires right up. I have checked the battery connections and they all look good. Am I missing anything?? The bike has the Dobek box on it as well.
 

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I had a similar problem that has taken my dealer almost 6 months to figure out. apparently there is a production line tab welded to the frame somewhere under the gas tank that rubbed through the wiring harness and was shorting out a few wires. There is no service bulletin on it but the service manager was tipped off to the problem by a yamaha factory tech. they replaced my whole wiring harness at $300. for the part and 4 hours labor.
 

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Is the new battery reading 12 volts? Just sounds like the charger wouldn't magically fix a short, not a mechanic but seems like if it starts right up with a charger, maybe the new battery is junk. Unless... the harness has a weak ground that the charger is completing, then I guess it makes sense. :unsure:
 

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I had the exact same problem! 2 days later the bike quit all together. Ended up one of the pins in my ECU plug had backed out and wasn't making a good connection. I don't know why that affected the battery like it did but I've seen a few Rappys with the same issue. Check the ECU, It's in a rubber sleeve on the left side of the sir box. Remove the plug and make sure all the pins in the plug are good. Mine runs like a champ now.
 
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