Bleeding the Yanmar
It is almost impossible, for me at least, to bleed a Yanmar with the manual lift pump. Use the lift pump to first bleed the system, up to the high pressure pump. If you ran it dry, this will take some doing. You have to get all the air out of the lines and filters from the tank forward. When you get all the fuel, with no bubbles at the high pressure pump, then spin the engine over. Open the compression release, and be sure to shut off the raw water intake. If you fail to shut off the raw water, good chance of flooding the engine with water. Crack the nuts where the fuel lines attach to the injectors. You do not need to loosen them much more than one turn, two at the most. Spin the engine over in fifteen or twenty second cycles. This assures you of not overheating the starter. If you have two bodies available, you can watch for the bubbles to stop at the injectors. Any air at all in these lines, and the Yanmars just won't start, and there is more air in there than you would think. My personal preferance is an electric fuel pump mounted at the tank. This bleeds the system up to the high pressure pump in a matter of seconds. Still use the no compression engine spin to bleed the high pressure side. As a final thought, be sure to tighten the nuts at the fuel line/injector junction back down tight, and after it starts, be sure to check for any fuel leakage.