You may have to drain the whole system including fuel lines, and flushing the injection pump. The prime the whole system with fresh diesel.
The fuel system is pretty easy for the most part. Just time consuming. Especially draining the tank and removing the crud
I've had pieces of equipment gummed up over the years. I drained the fuel tank. If it's easily removable, then removing the pepcock after it's drained and steam cleaning the tank works pretty good.
Then had to disconnect fuel lines from the fuel pump. If it's standard fuel line, then I just replace it if it's clogged. It's pretty inexpensive and easier then trying to get the crud out of it.
The hard lines to the injectors, I disconnect them from both ends, and blow them out with compressed air. Make sure and use a back up wrench at the injection pump so the ports don't get loosened up.
Replace the fuel filter.
Do Not blow compressed air through your fuel pump or injection pump!!!!! You can cause damage.
Then I start the bleeding process. I get fresh diesel to the injection pump. Leaving the fuel lines from the injection pump to injectors disconnected. I crank the engine till I get good clean diesel out of the ports on the injection pump.This will also let you know if you have a blockage internally in the injection pump.
Then hook the lines to the injection pump but don't hook them to the injectors yet. I crank the engine over till I get good clean diesel out of the injection lines. This also makes sure anything missed by the compressed air gets worked out of the lines and doesn't plug the injectors.
Then hook the lines to the injectors but leave them loose. Crank till diesel spurts from the loose fittings and then tighten. This makes sure the air is out of the lines.
Then I proceed to try and start the engine
diesel treatment and an algicide are a must when filling the tank back up