I was real busy at work yesterday and now am at home. The needle and spring check valve arrangement isn't used on later pumps. Its my recollection (I haven't personally done this job in a number of years although we do them all the time in the shop. I meant to look it up before I left but my WIS locked up trying to print 202 evap removal insts for a freind in Tampa. I left the hour glass cranking and will seewhats happened when I get back.
Its my impression that the later cars have an encapsulated pump element check valve. There are plenty of things that went wrong including the posibility that a major leak from the brass seal will defeat the pump element check valve and cause a misfire by preventing filling of the line in question.
Another possibility in the pump is dirt. The pistons are driven upward by the cam in the bottom of the pump; sort of like valve in the engine. The pistons go back down due to spring force, also like valves. Like valves they can stick for various reasons.
All of this speculation is based on the fact that a particular cylinder is misfiring. If a problem occured due to the repairs this would most likely be the case. If the engine runs rough with random misfires the causes would be different and not as likely to be the result of repair.
As I stated before, diagnsosis requires identifying the condition and if a misfire the exact cylinder misfiring needs to be identified. If that cylinder is the one nearest the EGR valve, I would do a compression test. The problems with the 350 motor seems to be a compression loss due to the piston rod bending when a large chuck of carbon winds up in the space between the piston and the head and the engine has momentum.
If a single cylinder misfire is identified and the compression is uniform to within 10%. The pump should come back apart on atleast that cylinder to view the seals and assembly for correctness and I would crank the engine by hand and view the piston of the pump going up and down.
The real unfortunate part of all this is that everything you do on a diesel takes so much time and there is so little real diagnostics available.
Bosch Master, ASE Master, L1
33 years MB technician