The Briggs engines use a key on the crankshaft to locate the small timing gear rotationally. I have always assumed, on the basis of no evidence, that the camshaft and its timing gear are in one piece. If that latter point is true, I don't see how the valve timing could be wrong when the timing marks are aligned.
I can't understand your pictures of the ports and valve guides, so I don't know what problems you are seeing in those pictures.
From the marks on the piston above the top ring, and the stripes down the bore, it looks as if there has been foreign matter in the cylinder and that is the resulting damage.
