Gday Blackened,
From your description, you will need to take the fuel tank out & flush it out, otherwise you will eventually get crap again around your pump.
The other thing I would try is pull the rubber hose fuel line off the intake at the pump, put a piece of plastic hose about 1 - 2 feet long, fill with clean diesel, have someone hold it up or put it in 2 - 3 litre container, bleed pump then start.
This will eliminate any air leak you could have in your line from tank, as you could be sucking air but not leaking fuel. If this is the case you then have to pressureise the tank to find the leak.
If still no improvement, I would then get the injectors serviced.
If still no improvement, its got to be the pump, which may have got some crap in it whilst driving around with crap in the tank & low fuel levels.
Jack