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There are two pumps inside the FSM on your engine, one is high pressure feeding the injectors the other is a boost pump drawing fuel from the tank. Without scanning the engine I would say the running issue and the alarm are due to the boost pump timing out. This would trigger the guardian system to slow the engine down. Bringing the throttle back to idle and allowing the FSM to fill again would allow just a few minutes of higher RPM. To test this, you will need to remove and open the FSM on the engine, then apply 12V directly to the boost pump and check its running. With the boat sitting that long, I would also replace the fuel line from the boat to the engine and all fuel filters.
While the FSM is open, the float should be updated and the MAP reference hose should also be replaced. This will ensure that there are no issues with them going forward.