I'll tell ya before getting yourself involved in a huge project, have you isolated what the problem is when you're in a failed (not running) state? Easy enough to quickly determine. You need spark, fuel and compression. Check all three, although I would venture a guess your compression is probably fine. It's expensive and time consuming to throw parts like darts at a symptom, and let's face it what you describe could be caused by a number of issues that could be both fuel or spark related. What I did when I had a similar problem with my boat was to take it out, bring some tools with you and a chase boat. When the thing conks out, determine what your lacking and go from there.
I would based on what you describe be more inclined to think you're dealing with an ignition/electrical problem but that's pure speculation. Since you've stated the boat has seen salt water simple connector corrosion could be the culprit.
Fuel delivery problems usually occur at any operating temperature and symptoms get worse as the engine is asked to run faster. FYI - with a two stroke a fuel starvation condition is bad, leaning out a two stroke to much for a period of operation, especially at operating speed can do damage to the engine leading to scoring of the cylinders and possibly lead to seizure even if it's got an oil injection system.
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