Merc 3.0 stalls
I had same senario, however, I had a 4.3L Merc.....
Engine would run fine for 15-20 minutes then cough and stall....
After several trips to marina, and many dollars spent for things I didn't need performed, I found the underlying culprit either from NoBozo, DaveR,
Ishoot308, or SIKSUKR can't remember? Lot's of experience in this group for sure !
But the issue was the coil ! As NoBozo described so correctly quote.., '
Faulty ignition coils can overheat and short out internally....Then recover when they cool off'. This is 'exactly' what was happening.
Marina said it was gas related (ethanol), but after draining the tank, then filling with fresh gas, didn't resolve the issue. They then did a carb rebuild, again, didn't resolve the issue $$$.
After feedback from this Foum the common denominator was 'coil issue' ! I ordered a new coil for $35. and installed myself in about 30 min. Problem solved ! And the boat was running like a race horse again.
So, I still think you have a spark issue, as a result of a bad coil.
Oh, one last word, make sure you use a marina with a good reputation, and not just 'parts changers', who try this and that, as a process of elimination to resolve the issue.... Lessons learned !
Bigdog
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