Maybe I missed it, but where is the holed 13B piston?
The 13B / 13B-T is a great engine but the issue is parts supply. As far as I can see, Toyota has stopped making almost all 13B specific parts. They are a generation behind the 3Bii / 14B / 15B engines which have much better parts availability, but which share few components with the 13B. My main worry would be your cylinder head - if that is damaged beyond repair your options are basically used or maybe a Made in China replacement. Pistons and rings should be available as Japanese aftermarket items. Crank can be ground and block rebored if necessary. Rebuilding that engine will be an expensive process I'm afraid.
With the old 3B - I would just run it. Cracked pre-chambers are very common, catastrophic failure from them disintegrating is (very) rare as far as I can tell. As long as you don't put a turbocharger near it, the 3B is an incredibly reliable and long lasting engine. Hope you can get it running reliably.
Where is this melted hole? If you mean the almost perfectly circular depression in the top of the piston, then no, that is not a melted hole. That's effectively the combustion chamber on a direct injection diesel which doesn't have pre-cups (hence why they are more thermally efficient and far better suited to turbo charging than an indirect injection diesel).