Years ago we had a Sun Runner Ultra252 with a 5.7 Volvo. I was getting stumbling issues, usually after warmup, and above 2800 rpm or so. I initially figured the air gap between the HE sensor and trigger wheel in the distributor was the culprit, as making adjustments helped, sorta. I ultimately found THEE problem: Whoever installed the distributor had it clamped down with part of the gasket in the hole. This meant it was clamped down at an angle, and was putting pressure on one side of the shaft and bushing. This is the bottom of the shaft and it's bushing. Worn so badly a paneling nail would fit!
The upper bushing was also worn, just not quite as bad. But it was bad enough that the shaft was vibrating and wobbling, to the point the air gap at the HE switch would vary so much it would misfire badly. I replaced the distributor with a Mallory Unilite, and the boat never missed a beat after that...(also changed out the Holley for an Edlebrock, but that's a different story!)
Might not be YOUR problem as this was a pretty unique situation, but I do believe your problem is related, especially if you had the carb *reliably* rebuilt. If the gas flow is good, you're certain the float level isn't too high and the carb is clean, but getting jostled around by waves causes your engine to misfire, you almost certainly have a bad or loose wire or component somewhere at or between the coil and distributor. Twice in my life I had cars act like that, and the problem turned out to be a broken or loose ground wire in the distributor.
Some 'components' come to mind: the HE switch in your distributor (I'm assuming it's not a points-type distributor), the ballast resistor, if you have one (both of these correlates with the sync gauge issue), and just maybe, spark plug wires. I can also attest to having spark plug wires go bad more than they ever should have, just recently I pulled the tranny fluid stick out of my Wife's '89 Mustang while idling and got knocked on my butt by a spark plug wire, with less than 15k miles on them. If you have a spark plug wire leaking, jostling the boat may put it in contact with a riser or another wire and cause a misfire.