You're car sounds like it has almost the exact symptoms mine had/has. Been babying mine for over a year and it's just now coming around. Previous owner ran WVO. I don't know the setup, but it was wrong.

Anyway, some things I've done to correct it, in no order:

Filters
Diesel Purge a couple times
Engine and trans mounts
New Monark nozzles, balanced
Delivery valve seals
Rack damper pin
Cleaned switchover valve and lines
Many valve adjustments (lots of crud on seats it seems)
Lots of MMO and PowerService Diesel Kleen in the fuel
Should have done a MMO cylinder soak - may still

She has shown improvement in stages over the last year plus, but didn't really come back to life and smooth out until a month or so ago. Knowing that things were pretty solid I finally took it up to 90+ mph for several miles one day. Different car ever since. Some days she still sounds better than others, and she still has a little 'wop' at about 1000 rpm (always been the roughest spot vibe-wise), but it's vastly, VASTLY improved.

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1984 300D Light Blue/Blue
2006 C280 Silver/Black