Has someone looked into it to see if the fuel is clear enough to see the bottom of the tank? Do you just have bad fuel? Why would you use "off road" fuel? Is that just #2 heating oil or did you get some more "gritty" stuff?

Since I haven't seen many boats with diesel inboards that don't have RACOR/Parker filters, I'm not sure about injectors being damaged. Usually I would expect the engine just not to start or (in your case) both cylinders being affected.