Can you post a youtube video of the knock for others to listen to?
The reason I asked about the oil leak was because a serious oil leak can reduce pressure perhaps causing a bearing to fail. Doesn't sound as if that was the case. Did you use the same oil cooler for both engines? If so, could some contamination have passed from one to the other?

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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