I must be missing something. All I would do is use the pencil plugs in the new engine, make jumper wires to go between them and hook the one nearest the firewall up to the wire that energized the former loop plugs. I don't see why you need to replace the relay.
Now wait a minute, maybe the issue is that the old relay has a temp sensor wire going to the engine on the old system and no temp sensor system on the new engine? If so, I think you should be able to swap over the old temp sensor, or operate the old relay without a temp sensor?????

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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