Have you checked the exhaust elbow yet. It will rust and clog up after awhile and is to be changed every few years so I am told. I had similar problems as you. I found an oil leak on the external oil line, antifreeze from the water pump and had a barnacle encrusted prop. It was an adjustable prop and when I serviced it I did not set it right and it ran worse than ever. I reset it properly and it runs fine. My exhaust elbow was so blocked I dont know how water got through. At higher RPMs I also had a foul oil smell that is now gone. From what I read that alot of yanmar 2gm and 3gm30 are over propped and never get to cruising rpm before they start smoking.
That derelict boat was another dream for somebody else, don't let it be your nightmare and a waste of your life.