I think it would more likely be a loss of compression (leaking valves or rings?) than a blocked exhaust otherwise it would probably show up in bad running once it started, GrumpyGel.
Re-check the work done on the HP pump and try to check the injector and glow plug sealing for leaks? Also, check the fuel rail pressure sensor connector for corrosion, although I would think that would also show effects once the engine was running rather than just on starting. Random thought, but what is the condition and history of your battery?