Electric pump in addition to an engine mounted pump? Or in place of? If you try to "prime" or run the electric pump without the engine cranking, you run a risk of flooding the exhaust manifold and spilling water back into the engine. You can hydrolock the engine in this scenario, so you need to be CERTAIN you are not doing this, as you can create significant damage, ex. bent valve, bent rod, bad juju. If you suspect this is what's going on, pull the glow plugs and crank the engine to blow the water out of the cylinders. If you do get water blowing out when cranking, get it all out, check the oil for water. If no water or oil isn't milky, then get the engine running and run it under a load until it's warm, then change the oil. If water was in the cylinders, some will get into the crankcase, and the oil & filter should be changed. Running it will help clean the water out.
The "running bad" coupled with the electric pump is what triggered this thought. There's no way the pump will "strain" the engine to the extent that it will bog. Some of the Westerbeke's are known for seawater pump issues, yours may have had the electric supplemental to overcome some of that? If the seawater pump has been run dry with engine running, it may have eaten the impeller blades. If so, you need to check downstream of the pump and remove any debris. Pull the caps on the exchanger, that can give you a good indication of cooling system health. Those pumps are also prone to reduced flow due to worn cover plates and/or cam, as well as the back side of the housing. The cover plate should be replaced when it shows visible signs of wear. Keep a spare, they have unlimited shelf life.
Define the problem.
