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Do you have the service manual for this atv? There is a download on here, somewhere. You’re absolute best bet is to get that. Go through how to get the trouble code section and see what it says about how many flashes you get. That’s the very best way to start. If not, you’re throwing darts blindfolded.
 

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I know Im a little late to reply but, if nothing else its the ECM... thats what it turned out to be on mine... the shift motor circuit (which is INSIDE of the ECM) somehow got water in it and shorted out, which prevents the hondamatic system from sending a signal to the shift motor (so the signal will make it from the shift sensor or shift button (depending on if your in auto or esp) to the ECM but will not make it past there because the physical connection inside the ecm is damaged). Luckily I was able to bypass this and save myself from spending 300$ on an ECM by wiring up relays between the shift buttons and the shift motor directly without the use of the ECM. I've attached a diagram of how mine is setup (diagram varies slightly as there is only one + line going to the shift buttons and 2 + outputs (one from up shift and one from down shift)). Feel free to message me if you have any questions. Best of luck
 

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