The bore seems to have some vertical marks, which might suggest that the engine has been run without an air filter. It doesn't look too serious, but the marks will need to be honed out and of course the rings replaced. The piston may have matching marks, which doesn't necessarily matter much. Are these old pictures? I thought you put that connecting rod in the engine with the knock and the misaligned rod?
I suggest you take a look at the valve seats, since it was hard to start. It's easier to do these things while it is in pieces.
