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I am here and just reading through your post now, just a sec.
Possibles: It could be sucking air.
It could be the injection pump actually being bad, which it could very well be.
Sucking air means to fix: you need to put a clear line in place of the fuel filter return hose and check for air bubbles in the system.
If there is no air in that return line, take the return fitting off of the fuel injection pump. Remove the straight adapter that is between the elbow and the pump get a white sheet of paper clean and tap the fitting on the paper looking for bits of metal. If there is bits of metal on the paper, then you need a new injection pump.