It's a case of "you get what you pay for" and your priorities. A bike that's been in your family going on 35 years doesn't sound like a candidate for a cheapie resotmod. You could source a PRC clone motor on the cheap. Converting the 12v isn't difficult; modifying the wire harness might be, if you're unfamiliar with electrics and, the mod would be more, or less, permanent. The rest of the conversion would be, essentially, bolt-ins and easily reversible. I'd have to at least ask how important things like running, shifting, overall smoothness/durability and broad parts support are to you; that's where the original Honda motor has it in spades. Plus, it's, well...original and all that comes with it.
If you're going to do the rebuild, then figure on roughly $350 in parts, plus machining (bore/hone & valve job). A crank rebuild, if needed, will likely add $175; you could source a better used crank from another 6v 3-speed CT70, or a 6v Z50...which would be a lot cheaper. The rest is time and elbow grease. If you farm it out, plan on spending $700-800 to get it back in show condition, ready for the next 35 years. The total cost spread will be less than $500, probably A LOT LESS. Sounds to me like your clutch & transmission are in decent condition. It's up to you to decide which way is best.