Are you so sure it's a fuel problem? It could be an ignition problem, have you checked the spark? People blame ethanol for everything these days. It's not always the problem.
You said the boat ran great on a few short trips but gave you problems when you stoped for a swim after a ride. It could be a heat issue, while you were swimming the engine was sitting there wrapped up tight. Could be the coil. What does you temperature look like when you're crusing, could you be overheating? When did you last check for a worn impeller?
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