The fuel may indeed be causing problems. Regarding changing of the Inj pmp - I neglected to mention what are probably obvious steps, such as good cleanliness i.e. remove debris from fittings before diss-assembly, etc. , also covering any openings in the fuel system with baggies and rubber bands to prevent mositure and dirt from entering, things like that. Frankly some people do not have the timing checked/adjusted if the engine operates properly after the inj pmp change. But depending on your point of view, the "most correct" way to do it would be to have the timing checked by an experienced diesel mechanic with the proper diesel timing device.