Fuel systems in these old MB's is designed for a diesel formulation that does not exist anymore. Lubricity from sulfur at 15ppm is a far cry from what was used in 80's and 90's. Use of ATF to fill a FF is probably providing a short term lube effect to the IP that will quickly be negated by running diesel with no additional lubricity additive. According to the Spicer report TCW3 Two stroke oil has a higher lubricity rating then ATF, IMHO probably a better choice for filling a filter then ATF (also an excellent choice as a low cost lubricity additive for fuel if Stanadyne, PS, or Bio are unvailable or deemed to expensive)
On my TDI before every 2nd OC I hook up a temporary fuel can and run engine on pure Diesel Purge (1 can) to clean the IP, also add max does of Stanadyne at every fuel fill-up.