My guess is that you have a leak somewhere in the fuel line, and it's probably on the suction side which is why you are having trouble finding it. Check all aspects of your primary filter setup and all your hoses and fittings from the tank up through the last pump you have in the line (if you have a mechanical lift pump, that's probably the last in the line, even if you also have an electric pump). For instance, some of the Racor primary filter setups have a plastic screw cap at the top of the assembly. If that cap has a slight crack, you could be sucking air right there. Not enough to bother you with normal operation, but when you get on the thing or it's working harder because of conditions, that might be enough to make it buck. (Take a guess as to how I know this.) Same could be true with a loose connection with a hose clamp, or a pinhole in a fuel line on the suction side (not likely to be on the pressure side because you would be spitting diesel out of the hole and it would be easy to find).
My guess (and obviously that's all it is) is that it's not the fuel. You've refueled a few times, and if it was fuel you'd have the problem regardless of conditions (save for the possibility of churning up junk from the tank, but you'd know if that was the problem when you changed the filters; they'd be clogged with all kinds of nasty stuff).
Another possibility, but I bet this isn't it, is that you might have a screen on the bottom of your pickup tube to the fuel tank. When you're banging around in seas, the junk gets sucked up and clogs the screen. When things settle down the junk falls off the screen and you have better fuel flow. It should be easy to check. Just unsrew your fitting on the tank to which your fuel line is connected and pull it out of the tank (the pick up tube should be connected to the fitting and just lift out). Take a look at the bottom and see if there's a screen. Also, doing this will give you a sense of whether you have algae in the fuel, as the pickup tube itself will have slime on it.
Generally speaking, fuel system problems are easy to find, with one exception, and that's a leak on the suction side. So, if you've tried a bunch of things and can't find it, I'd look hard at every component on the suction side. If you have one, a vacuum gauge ought to tell you if that's your problem too.
Another thought, which hopefully won't be the situation, is that you have bad compression in one of your cylinders. Hard starting and rough running often is a sign of that. That could be caused by a bent rod or a variety of other things. You should hope it's not that, as that will be a more involved (and expensive) process to fix.
All that said, I don't have experience with Westerbeke engines, so it also could be something anomalous to them, in which case ignore all of the above.
Keep us updated. I'm curious to know the conclusion.