Finally I got my head back from the machinist, with the new black diamond valves installed.
I was going to smear some clay on top of the piston to be sure the valves weren't going to hit, but I dug out my box of sculpting clay and found it had dried out completely. So I shined a bore light down the compressor hole while looking down the spark hole and rotating the engine. Maybe not the best test, but it looked like there was plenty of space in there when at TDC. There should be anyway, with the 2mm spacer at the bottom of the barrel.
Fired it up and wow... I was really impressed with how quiet the engine is now! Did my plug chops and put in some richer jets. Hope all is well from now on!