I don't have any amazing magic things to add to what others have said, but I would STRONGLY discourage you from fiddling with the idle speed adjustment on the injection pump. The inability to run stably at normal idle speed is a symptom, not the first cause of a failure.
This is not like the mixture adjustment on your outboard carburetor. It does not control the fuel flow itself, rather it controls the set point of a speed governor than then in turn adjusts the fuel rack. Adjusting the idle speed adjustment is not typically done as part of a repair, but is part of the set up of the injection pump.
If you can get the engine running at a stable speed (slower is easier for this test) it might be worth opening the nut on the injectors, one at a time. When disconnected, each injector should have a similar effect on the speed/smoothness of operation. If one has little or no effect, then that injector is likely bad or clogged.
Another trick that can help sort out things, put a piece of clear plastic tubing into the system just before the lift pump. If you see bubbles flowing by when running then you know you have an air leak that needs fixing. If you see only clear fuel flow, then you can check off everything upstream of this as OK. With your fuel tank nearly full, I doubt this is the problem, but it helps to be sure.
Last thing, I might have missed this, but if not yet done, changing the secondary fuel filter on the engine would be a good idea. Again, not a likely, but a possible, cause of this kind of problem. For this filter, I would recommend (if possible) using a Yanmar OEM filter. Some of the aftermarket filters have smaller elements and add excess restriction to fuel flow, especially after then get a bit of dirt in them. Normally problems with this filter are seen at high speed, not idle, but you have checked most all the easy boxes, so the less likely ones are what is left.
Tracking down fuel system issues like this can be a pain, but it will work out.