Hi Boeing,
Well I can say categorically that the cotter is shagged and also that PTO shaft is rather suspect.
Can you confirm if that's a definite crack adjacent to the key way ? if it is I would say it's curtains for that crankshaft and replacing the whole engine would probably be the easiest option, depending on your mechanical ability I guess.
The clutch body will most definitely be flogged out and require replacing especially with it running with a shot captive cotter like it was.
The thrust bearing would probably be ok even though it sounds rattly I would clean it out in clean petrol and dry it out then soak it in oil and allow it to thoroughly drain and after that you'll find it should be ok for another battle.
Remember that the bearing will run smooth when the centre race is pushed in and rotated and not the opposite direction as many people evaluate.
I'd like to see some really good close up photos around the engine mounting points on the two rails.
For now,
Cheers,
BB