Not real familiar with waverunners (this is a car and truck section after all), but remember that when you have been riding and stop engine it gets much hotter. Could possibly be coil "Heat Soak", or even a fuel system vapor lock issue caused by a pinhole leak in a line or a bad gas cap. Not very confident in this, but the best I got. Try posting in the waverunner section.
SOURCE: Intermittent Starting Problem
You have to determine if the problem is loss of fuel press or a los of ignition spark when the no start occurs, I suspect the fuel pump.
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