Regardless of what some may say here there are specific ways to bleed Yanmar motors. Yanmar America has one way and John Deere has another. I used John Deeres method on mine and it worked. I have also used Yanmar America's method and it worked too.
Deere's method as per JD 750 manual (3 Cylinder)
loosen bleed screws on filter until all air is purged.
Retighten bleed screws
On 3 CY motors loosen #1 and #3 delivery valve holders 1/4 turn( these are on top of pump where injection lines attach to pump)
Loosen all injection lines at nozzles
Fuel will gravity feed from tank to fill injection linesYou are saying that fuel will gravity flow from the tank, through the injector pump and through the injector lines all the way to the injectors. I have had some people tell me that nothing can flow through the pump, that it must be pumped out. If you are right and fuel can flow through the pump one way then it could also flow through the pump the other way and this means that if an injector was leaking compression through it, then the compression could flow back through the pump into the fuel line creating bubbles. If this is indeed true, it makes more sense because the bubbles are appearing mostly when I let off on the throttle and the pump is not pumping much fuel, maybe allowing compression to back flow through the system. Even though they checked my injectors to make sure they were popping correctly, I don't know if they could tell if they were leaking back compression. Maybe I should buy one new injector and try it in each of the cylinders to see if this corrects the situation. I do hate to spend $100 for an injector just to test with if this is not a realistic possibility.
When fuel appears at injection nozzle tighten injection line to nozzle to proper torque and tighten the approperate delivery valve connection on pump. DO NOT TIGHTEN FUEL LINE #2's INJECTION LINE AT NOZZLE YET! (For 3 CY only)
Push throttle full on and start engine. It should run on #1 and #3 cylinders.
When fuel appears at #2 injector stop engine and tighten injection line at nozzle.
System is bled!!
NOW I am going to beat a dead horse again
Govenor!! Get a manual on these gadgets. My JD manual in very informative.
Did you know the govenor over fuels motor during startup? It can do this because counter weights are not spinning. By overfueling during startup the engine appears to run correctly until overfueling stops and govenor starts working with respect to a started engine. This is where I think you have issues. Please take a second and thrid look at govenor.
I am an amature and having looked at the manual for the governor, do not feel that I am qualified to remove or repair it. I also have difficulty understanding how the governor could make it run bad until I put the air bleed line on it and then allow it to run OK.
Next you need to make sure pump is timed correctly. Just like any engine it can act different when cold. If timing is off too much it could start when its cold but not want to run once warm.....
My engine starts immediately when cold or warm and runs perfect except when air blocks the fuel line. But I still am leaning toward govenor