Check it out.
The year of your engine is probably the same as the boat. I don't recall a Westerbeke 13 but there were a couple of 12's. If we have to go beyond the scope of this response, we will have to zero in on the actual engine. All that you say could fit. The 3000 RPM under load on one cylinder might be marginal. To check how many cylinders are firing, get the engine to operating temperature and the "crack" the high pressure fuel lines where they go into the engine, one at a time. If both cylinders are good, the engine should slow down equally for each injector opened. If you detect no change on the first one, the second will stall the engine, right away. (or vice-versa) If this shows that both are firing, you either live with the shakes or get a lot more technical. If only one is firing, you must determine if the problem is in the injector or the pump. This can be done by swapping the location of the injectors and redoing the test. If the problem changes cylinders, its time for injector repair. If not, more expertise is required to service the pump.
