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ok good info and this aligns with what happened initially. The boat would idle for about 2-3 min and then alarm. turn it off and turn it on and alarm would go away for about the same time idling. Anything over idle did not trip an alarm.I have an 04' 225 for 22 years, no ecm issues. The only regular issues with that generation of V6 are 02 sensor, vertical shaft bushing, crankshaft thrust bearings and corrosion issues. An o2 sensor issue will trigger an intermittent alarm after idling for a few minutes. o2 sensor only affects a/f mixture from idle up to 2500rpm, all map after that.
Easy test for o2 sensor, launch the boat and get to open water. turn off the engine for a few minutes then restart and immediately accelerate to over 3000 rpm and keep it there. If intermittent alarm comes back its either water in fuel, charging or battery issues.
A steady alarm is serious, either overheat or low oil pressure, stop engine immediately. Find another mechanic, running DR H diagnostics will tell you exactly what's alarming. The first thing I would do is check the fuel pressure at idle and under full power. If you do need an ECM they sell them all the time used on ebay.