Any updates?

How many hours on the engine? I had to trouble shoot an engine this summer that was doing pretty much the same thing. So I ran it at idle and pulled the spark plug wire off the distributor one at a time to see if all cylinder were firing. 2 weren't. So I checked the compression, I found that those cylinder were low. I pulled the heads off and took them apart and it was the valves that were "mushrooming". Some of them started to cave it and when measured, my worst one was 0.239" longer than the shortest one. The engine had over 700 hrs on it.
So my advice to you would be to start the engine, run it at idle and disconnect the spark plug one at a time and listen to check if the engine sound change and if you find one or more, check the compression.
If you're lucky, it'd be valve fatigue only. If not...

Install a fuel pressure gage, that will tell if it is fuel starved. I would guess the pickup or anti syphon valve if pressure drops.

If its a lobe on the cam it will tick intermittantly then quiet. If you have ticking, cut the oil filter open and look for the flakes of death. I highly doubt the timing chain jumped.

As far as ignition goes, double check everything. Pay particular attention to the rotor and assure it doesn't have a greasy paw print on it.

BT

Don't know if your boat is equiped with a rev limiter, but if so, check that. I have been tracking down a problem with one of my engines breaking up and finally tracked it down to that. Mine is a MSD and when I disconnected it, it ran great. Only took about 2 months to find it.

power valve in the carb

are there any non-mercruiser wires connected to the coil?. A compression test should tell you if you have other mechanical problems.

need to pull valve covers and check cam or valve springs,sounds thats were your likely going to find your problem

I had a similar issue and after several months of troubleshooting, replacing this and that, it turned out to be a leaking intake gasket on the bottom side which caused a lean condition on two cylinders.

Rick

What was the outcome?

I have a similar issue above 4000 rpm and after a season of electronic and fuel troubleshooting, have narrowed it down to either a leaking intake manifold gasket causing a lean condition on two cylinders, and I also suspect some valve float due to either not enough closed spring pressure or coil binding. I have the intake off and see the bad gasket and the springs are suspect because I changed the camshaft to a slightly higher lift and did not change the springs accordingly.

Rick