Hi -
I would not suspect pump timing initially, it is possible but highly unlikely. I would do a compression check on the engine and make sure it's at least 350 PSI, and if so I would have the injectors cleaned and adjusted by a diesel injector company, or replace them.
Injector timing and slop in timing gears is not a simple thing - I would suggest getting a factory manual that discusses the specs on the gears, and timing the crank/cam/injector pump.
Good luck!