I had an issue that was kind of similar on my 99 GP760. I believe the electronics are very similar.
I lost the ground to the electrical box. I fixed it by running a ground wire to one of the mounting bolts for the electrical box. If you have a volt meter or a test light, hook it up from the positive of the battery to the mounting bolts for the electrical box. You should read the battery voltage (usually around 12.5 to 13.1 volts with it not running).
You can try shorting the negative side of the battery to one of the mouting bolts for the elctrical box and see if it comes to life. The elctrical box should be grounded, so shorting the box to ground should not hurt anything. Inside that box there are two screws that all the ground connections go to. If the box itself isn't grounded, then nothing else gets a ground connection.
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Current PWCs: '99 Yamaha GP760, '95 Polaris SLT750
Previous PWCs: '88 and '89 Yamaha WR500
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