My questions/observations:

1. If the pump was never re-timed to compensate for the stretch in the timing chain, it shouldn't have to be re-timed with a new chain unless someone for some reason pulled the pump to replace the chain.
2. How in the world do they know there's diesel fuel in the oil? Did they send it out for analysis of some sort?
3. There's one big O ring on the front of the pump that MAY have to be replaced if the pump is removed. I replaced the one on mine, easy as pie.
4. If you really have to get the pump rebuilt, I'd look into performance elements. I'd suspect that an aftermarket rebuild with performance elements would be cheaper than a factory job and the shop that does it will be someone who's an enthusiast, not just a lackey.
5. Did the hard starting and whatnot start after the chain was replaced?

Oh, and the only thing electronic about the pump is the rack. Timing is as mechanical as mechanical can be. The computer algorithm is pretty straight forward. It looks at intake air temp, RPM, MAP and throttle position and then makes a decision about how much rack it will give you and not generate an inordinate amount of smoke.

__________________
-Evan


Benz Fleet:
1968 UNIMOG 404.114
1998 E300
2008 E63


Non-Benz Fleet:
1992 Aerostar
1993 MR2
2000 F250