If it was my bike, I would be sending the cylinder out for work and I would do some work to smooth out that cylinder head. Get some scotchbrite on those dark areas to see if the scoring is 'fingernail sensed.' Is that pitting in the cylinder walls at the intake port?
Something terrible happened in there at one point, but the current piston is certainly post cylinder head damage.
Hows the piston look? You can see the skirt through the intake and exhaust port. (if you don't want to disassemble yet)
I would do a top end and check bottom end specs. Shouldn't be too expensive, you caught this one before any real damage occurred. -BIG DAN