You may have a clogged injector so that the fuel isn't atomized completely. Try pulling the injectors and cleaning the tips. You can probably just clean them up carefully with a wire brush and solvent. In the worst case, you may actually see a charcol briquette stuck by the pin hole where the fuel gets atomized. There is a picture on page 42 in the
Yanmar Operators manual on what the spray should look like. A diesel repair shop can "pop test" the injectors.