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Hi Matt, my name is Jason.
Have you had the engine hooked up to Yamaha's diagnostic laptop in order to pull codes yet?
Unfortunately no, the code reader is proprietary to Yamaha, and automotive code readers will not work. Yamahas system is called YDS, Yamaha Diagnostic System. Its' a laptop based system. It's not to terribly expensive if you wanted to buy it, but that is the only way to pull codes out of the engine. Click this link, this is the system - http://www.ebay.com/sch/i.html?_from=R40&_trksid=p2050601.m570.l1313.TR12.TRC2.A0.H0.Xyamaha+yds.TRS0&_nkw=yamaha+yds&_sacat=0
Was there anything else Matt?
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If I (or anybody else) could fix alarm problem without hooking up the diagnostic laptop to the engine then there would be no need to have a diagnostic laptop. I think maybe your expectations were a little to high here.
Hello, my name is***** will assist you.
You gave all the clues. when you add fuel from a marina, allot of times, what you are getting is water mixed in with it. This would cause the alarm on the water sep filter on the engine. Look closely at it and you will see that there actually 2 layers inside it. the bottom being water. and since you have water there, there is water in the fuel tank of the boat. you will need to call a local company that can "clean" fuel in a boat tank, Basically they recirc the fuel through several filters to remove all water and debris from it.