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Hi my name is Mike,
Two beeps every minute on your motor means you have a sensor failure... this could be one of a few sensors on the motor. The only way to know for sure is to plug it into a diagnostic scanner. The good ones are very expensive so unless you plan on doing all the diagnostic work on your boat it would be more practical to get it to a MerCruiser dealer. If you are somewhat mechanically inclined you could just ask them to scan it and tell you which sensor it is and replace it yourself.
I hope this helps as it is all I can do for you without being there with my scanner. Let me know if you have anymore questions and I would be glad to assist.
For your purpose I might recommend trying the one from Sierra. It's designed for marine engines and although I haven't tried it myself, I have heard that it works well. The reason the motor cut out and died is because one of the engine's sensors is failing and sending a bead signal to the ECM and confusing it.
I use a professional diagnostic software with a special laptop but it costs over $3500. The sierra one is inexpensive and will give you a code that you can look up to see which sensor failed.
I hope this helps, If you feel my answer was helpful please don't forget to use the rating system to except my answer as this is how we are credited for our time.
sorry, here is the link to the Sierra scanner tool..