Im curious ab this as well.
My buddy bought my banshee and ran it wide open in 5th gear not knowing it was a 6 speed and the right melted it down. I tore into it and the right piston was chewed up the left side looked great.
I tore it apart for him. He had the cylinders bored 0.25 and new pistons. I just put it all together, got it running, heat cycled it a few times and its great.
But the bike is all original and had never been rebuilt. So i guess the bottom end is still good.
If I were you I would buy a complete bottom end that is good or a whole motor and start over.
You seem knowledgable do the top end like you want with a known good bottom end.