A couple more things that might affect you fuel injection performance.
The fuel injection pumps usually have a check valve on the top of the barrel - just below the outlet to the injector line. These can be no more than a conical disc shape with a flat seat and a spring on top to close the valve after the pressure has dropped low enough. These little check valves wear and the seats pit - sometime small bits of "stuff" get stuck under the seat, preventing these from closing properly. You only have three, so it would be important that they work properly as it makes a difference to the fuel injection pump operation. A fiddly job but often makes a big difference to the pumps operation.
Fuel injection pressures vary with the makes, running anywhere from 1800 psi to 2400 psi opening pressure. The spray should be a mist and you should hear a screech from the injector when the nozzle opens.
Lastly, do you have the means to work on the injectors ? You sound well informed on engines, so I would suggest you try taking one injector apart and look at the parts inside. If you do this, cleanliness is of the utmost importance.
The injector nozzle should mate to the injector body (depending on the type of injector as they vary a lot) and where they come together should be absolutely flat. They are lapped together with very fine grinding compound and the washed clean with diesel.
The nozzle and needle need to be checked for wear and should not be loose when together. Also the tip or point of the needle should be in good condition and again, lapped in carefully. To check for wear with the nozzle and needle, hold the nozzle at 45 degrees and the needle should slide down/out very slowly. If this happens, the clearance is not excessive and the needle should work just fine. If the needle falls out quickly then the nozzle and needle are too worn to use. The clearances for these are very fine and if you hold the needle in your hand too long it may not fit back into the nozzle (expands with the heat from your hand).
If you have the yanmar book it might detail some of the parameters for you. It might also pay you to spend a few hundred dollars on new injectors either from the dealer or a fuel injection shop. If you go this route DO NOT use reconditioned injectors as they are old injectors that have been worked on. New is the only real way to go. I would expect that they would cost around $400 for new injectors and new copper seal rings etc.
Good luck - sounds like you have narrowed down your problems to basically injectors !
Please let us know how you made out.
One other thing - is there an inlet filter or screen on the injection pump ? If there is a screen it could be that it is so dirty that the pump cannot do it's job properly. On my F250 diesel, the Stanadyne DB2 fuel injection pump has a conical, fine mesh metal screen on the inlet from the fuel filters. These can and do get plugged with debris.