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Hello my name is ***** ***** I will assist you. The problem you are describing seems to be linked to fuel starvation. Best thing to start with is to try the boat using a separate fuel tank and line and see if it makes any difference. If it does then the problem is due to a blocked / clocked fuel line. Check the above and let me know.
Ok next thing to do here is to check for spark on all spark plugs, see if there is a side of the engine (3cylinders) without spark and let me know. If there is spark check the fuel lines from the priming pump to the carbs. Make sure the pump sucks fuel from the bowl and delivers to the top of the carbs as otherwise it will flood one particular carb reducing power.
Ok , had a similar issue with one of my clients which ended up being a defective wire going to the switch box. I suggest you check all the wiring that have good continuity from one end to the other. Also if possible when the problem occurs check for spark then as it may be cutting out on some cylinders.