Best replacement pistons for stock '69 engine

Yes. Take Measurements First.
JBurch used 68 cc, but he's just estimating. One book says '69 could cc as low as 60. That's the minimum spec and you'll never find that on an untouched original. Chamber volume measurement isn't that difficult. Well worth it IMO.

Since the machinist had to go .040 over on the bore and you say the pistons have 4 valve recesses, it is likely this engine has been rebuilt once before. I would not assume anything. Its possible the heads are not even from a '69 318, although the book show the same casting through '74.