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Hi my name is ***** ***** you have a multi-meter ?
OK good, I need you to get me some readings on the battery, I will list below what I would like you to perform and then get back to me with the results.
If you can get back to me with those results. then we'll move forward from there.
Thanks Walter, with the unit turning over and if you are correct with a voltage drop only down to 11.4 VDC says to me that the battery is fine. As you pointed out this ski is used in salt water, at this point I suspect that you definitely have a connection issue, and it sure has intermittent written all over it.
I have to step out of the a bit, I see you say you have a 2009 VX110, if you don't mind give me the hull number and when I get back I can make sure that I grab the correct diagram and then I will go through that and give you the likely the best place to start, as far as reliability on the harness on this model they have been OK, plus Yamaha does pretty good with there harness's but that doesn't mean that you won't develop problems especially in salt water conditions.
Anyway I will get back to you a little later, I'm in California!