Update:
Totally forgot to give feedback on the question about the block. I cleaned it properly and could find no damage to the block anywhere. There were 5 studs that I did not manage to get out, but as the threads were fine I just let them in the block. Didn't want to break one off and deal with having to remove it.
The 9 studs that I did get out were replaced with new ones, coated with proper anti-seize on the block side.
Meanwhile I properly flushed the block and checked the head on a flat granite block. The head's a bit warped. I decided to try my luck and install it without having it machined. After coating both sides of the head gasket with a small film of Hylomar M the head + gasket were assembled and the bolts torqued in steps in the correct order.
Later I'll assemble the radiator and distributor and do a first warmup of the engine.
Is there a recommended temperature to tighten the bolts again or is just lukewarm fine?
Should the head be too distorted for the gasket to properly seal off I'll just dismantle it again. Now that all bolts have been removed and the head isn't backed on anymore that should go much faster than the first time.
EDIT:
While cleaning up the head I also removed two disc-like shaped *things* from inside the head around cylinder 2 and 3 on the outlet side. They had a diameter of around 2 inches and a thickness of maybe 1/4 inch. Only god himself knows what these things were, my guess is either severely dried up water pump grease or remains from an earlier repair of the head. Either way it certainly did not help coolant flow in the middle of the head, where temperature was consistently 5 - 10 °C higher than at cyl. 1 or 4. Maybe that was the main problem all along? We'll see...