I would recommend pulling the engine out of the frame. Then remove the gear box and split the cases. Take the crank out and turn it into a paper weight.

Inspect, and clean the cases as well as you can (inside and out). Clean as much of the water transfere ports as you can as well. Replace the studs that hold the cylinders on, get a new crank and put it back together. Depending on the cylinders, you may be able to re-use them (at least the lower piston looks good, so the cylinder may be fine). Check the heads as well. My guess is the upper head has damage, but possible not. Cooper is can be pretty soft so maybe it didn't destroy your upper head/cylinder.

But, it looks like you had water getting down into the crank cases. Probably due to the base gasket being so old.

Good luck, it's only a lot of work and money but you can make it run again I am sure.
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Charles Gallant