Well, if you're going big-bore, the edges of the chamber should be cut back, anyway. When doing that, it makes sense to bevel them, and that may be enough to 'erase' the piston-bang marks?
The cylinders: those abound, and are not real expensive (typically $50 or so). For the K1, any K0 diecast through K2 (even early K3, old factory engines) will directly fit. For that matter, any pre-1975 "K" model cylinders will fit, but the locating dowels on top and bottom would have to be shortened or replaced with shorter ones, and you would have to get a set of the 8 dowels and seals for the deck: the dowels are Honda parts about $1.50 each, and the seals come in the Vesrah gasket sets for K3-K6 engines (aka 1973-1976 "K" model kits is what Vesrah calls them).
I may have a set of rods (maybe more than one?). I might even have a K0 or K1 crank, although any of the pre-1976 cranks would drop right in. You will have to change bearings, would be my first guess, because the stress of that rod hit would surely damage the crank journal?
For a reasonable-cost solution that would certainly make all the ends "meet", I'd suggest:
1. Either: Wiseco or similar forged pistons 812cc or 836cc (or any of the 826cc versions, if you can find one) at high compression, with domed tops so you can carve away some of the chamber(s) around the edges to clear the piston crowns while still retaining compression above 9.5:1, or:
low-compression (flat-top) 836cc pistons and mill the head 1.0 to 1.5mm, then bevel the edges of the remaining chamber(s) to smooth out that ridge in the damaged one and make them all equal, not hard to do. Or:
get some oversized post-1974 pistons for the "F" or K7/8 engines, which have domes on top, maybe a step-bore size like 0.5mm or 1.0mm, and then reshape the edges of the chambers to accommodate them. I'd mill the head, too, and end up with 10:1 CR for a snappy K1, those engines like this sort of thing!
2. Valve job: this will recede the seats about 0.5mm or so and ensure plenty of clearance.
3. Replace the valve guides, at least in the clobbered chamber, as those will probably be cracked.
4. Get some new/used valves. Polish them up and use them for the new valve job.
5. Find some cylinders: lots of guys here have them lying around, and eBay sells them every day.
I am a cheapskate by nature, and like to keep rebuild costs as low as practical - but, reliable, too. Whatever you choose, use GOOD gaskets. Have the deck of the [new] cylinders milled flat, and the head at least this much, if not milled back some, so they will match and not leak.
How is the rest of the bottom end?
