I’m not super familiar with that engine but replacing the coil (not sure if it’s coil in cap or not, and I’m assuming you haven’t changed the cap and rotor as suggested since you said you swapped the alternator instead) may be worthwhile u less they’re crazy expensive.
coils can be tricky because they sometimes develop shorts only when hot. Engine starts and runs, then bigs down under load. Never had it happen with a boat, but I have had the problem with two motorcycles and if that sounds like what you’re dealing with, maybe worth a look.
you can always bench test it with a multimeter rather than go straight to replacing it; but that only works if the coil is shorted out even at room temperature. If course, if it fails a room temp bench test then you’ll have your answer.