You need to bleed the fuel system. I do not know about Yanmars, do they have a gravity feed fuel system or a pump? If you did not run it dry, you can crack the lines out of the fuel pump, (the ones that go to the injectors), and crank it or if it will start, start it. Crack one line at a time, you only need loosen it about 1/4 of a turn, if there is air you will get bubbles and fuel. Keep it open until the bubbles disappear, then do the next one the same way, and so on. If the tractor is running you should notice that the engine will smooth out and run as it should. It will miss if a fuel line is loose. Be very careful, the fuel comes out of the lines at very high pressures!!!! I hope this helps!! Good luck!!