Is the seal a rope seal, like we have seen before? If rubber, that is something new. U.S. 60's gas engines had the rope seal, but rebuild kits have a 2 piece rubber seal (better). But, nobody has reported that for an OM617 engine.

Rollguy posted a thread w/ photos about replacing the rear seal w/ crank in the block. Unlike U.S. engines, you can't just push the seal around since a pin secures it. Rollguy had to loosen the crank enough to get it out and the new one in. You can do it better and easier since your crank is out. As mentioned, roll the rope seal in until well seated. You can use a large socket or piece of pipe. I expect you must cut it and work on each side separately. I have never done a rope seal, just the 2-piece rubber replacements (U.S. engines).

I assume you noted that the connecting rods and caps have dash marks "/", "//", "///", ... to label which cylinder they were installed in and to (probably) orient the cap correctly. I don't know how much keeping them in the same location matters in a rebuild. More important is to keep the caps matched to the rods.

Note in the 3rd photo of post 46 how the oil chain tensioner attaches to the #1 bearing cap. That plastic tension rail tends to break. I found mine such. Haynes (and I recall the FSM) said you must remove the upper oil pan to replace it, which would be very involved. Nope, you just unbolt the bearing cap. Harder is removing the oil pump, but that is possible w/ just the lower oil pan off (search for my post). I suggest the OP replace that plastic tension rail since many have found them cracked at the pivot, about to fail. It costs <$10.

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1984 & 1985 CA 300D's
1964 & 65 Mopar's - Valiant, Dart, Newport
1996 & 2002 Chrysler minivans