Does your engine have glow plugs?


Is your hand priming pump, bolted directly to the "side plate" of the injection pump, close to the front? If it is, then your hand priming pump is on the suction side of the system AND it is possible that it might be sucking air thru it, or its gasket. (good place to start, by replacing it and its gasket = easy, too)

Note: If you have the type of fuel system, that I think you might have, then any excessive restriction, from the fuel tank, to the injection pump, will cause the system to suck air WHEREEVER possible.  just like previous posters mentioned about debris, in the tank, loose fittings or swivels, dirty filters, etc.  


Leaking fuel at the governor shaft area, may be causing problems, too. (other than just an external leak)  


Heck ,if your fuel system is the type, with the transfer pump, in the front of the injection pump cam, then even its lip seals can "suck air", too.

 (note: When it died on you, and you had to reprime it = signs of sucking air or air/combustion gases in the fuel system)