Valve adjustment is pretty simple so I would definitely do it and recheck the compression.
Have you replaced the fuel filters? Lots of black smoke is unburned fuel, so I don't really think it's a filter problem, but it's a basic item that is easy to do.
I don't think one low compression cylinder would cause the bad running you describe if other people's symptoms of bad cylinders are any indication. Perhaps it is a combination of problems such as bad fuel filters and one maladjusted valve.
Check the timing chain stretch when you are doing the valve adjustment.

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1977 300d 70k--sold 08
1985 300TD 185k+
1984 307d 126k--sold 8/03
1985 409d 65k--sold 06
1984 300SD 315k--daughter's car
1979 300SD 122k--sold 2/11
1999 Fuso FG Expedition Camper
1993 GMC Sierra 6.5 TD 4x4
1982 Bluebird Wanderlodge CAT 3208--Sold 2/13