This sounds like a problem we had a while back before ethanol. Boat slowed down and would barely idle after crossing rough water. We would wait a while and it would restart and run normally. After all the easy fixes like tune up, coil, intake gaskets, carborator gasket, I pulled the gas tank and dumped it out into buckets. Besides some water there was a surprising amount of debris. It was sucked into the pickup tube screen blocking flow.
This was a 1980 boat before ethanol problems caused all sorts of fuel problems but it is worth checking.
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