Geez, can I relate to this! I have a 98 Marquis with a C-12. My experience was similar but different. I had some instances of the engine "missing". I thought at the time, how can a diesel engine miss? Anyway, it got worse, so I called Cat, went to Cat service, they thought it was maybe engine mounts making the engine seem like it was missing, etc. I discovered that it was missing more on right-hand turns (as up a highway). Went on for months!
To shorten the story, it turned out to be a fuel temperature sensor that was intermittently shorting out the 5 volt supply to all those engine sensors. So, for just milleseconds at a time, the engine sensors shut down, then came back on. But, in my case, only in right turns.
Seems that the way that the cabling was tied together led to stress on the wire in right turns, leading further to a shorting of the 5 volt wire at the fuel temp sensor.
It took months of search, and only once I was able to get a service supervisor to ride with me and have the failure while he was in the coach could we prove to him that there was really a problem. Fortunately, during this ride it failed and continued to do so while we pulled into the service bay, left the engine running, in gear, while the computer was attached, and the analysis found it.
So, my message is, it is likely a simple solution, mighty hard to find, though! Cut all those tight cable ties around the engine sensors! Chuckle!! And mention this forum to the service guy!
Good luck!