I'm no expert on diesel engines, but it sounds like you might want to first make sure you are bleeding the system using the proper procedure for that engine.
Can you locate a user manual and follow the specific bleeding instructions for that model Yanmar?
I have a 3-cylinder Yanmar in my JD750. I replaced the fuel filter this past weekend so I was reading the bleeding procedure. The process described was a little complicated. The manual lists a series of steps, in about three different parts of the fuel delivery system, to be followed in a specific order. The instructions also mentioned some odd things, like NOT bleeding the line going to the middle injector.
Maybe none of the parts are bad and you just need to bleed it a certain way?