I had the exact same situation.
Bores cleaned up @ .040 but one needed 1 sleeve. I used the exact same new Silvolites that you currently have. They are a cast piston that installed at .017 above my deck. I redid my stock rods and used the original forged crank and did not balance. Engine runs strong and smooth. Like you, this is a punchy cruiser engine.
If it were me, I'd try cleaning the rust off with solvent and a scotch brite or some other mild abrasive. Any pits in the "stroke zone" and it would be off to the machine shop for me.
Good luck.