Booger me!
If the pistons were hitting the heads I'd expect to see a sort of shape to the denting, not just random scratches! Definitely looks like foreign-body damage, I've never seen anything like that...
BUT
The combustion chambers in the heads look fine, which would seem to indicate pistons touching.
I know you say the engine is sound mechanically, but here's a list of thing's I'd do.
1) get a straight edge (steel rule?) and hold it over the piston holes. crank the engine by hand to see if any hit.
2) if they do hit - worry. The block has either been skimmed too much or you have the wrong piston/rod combo.
3) if they don't hit, remove te pistons and rods and check for slap. Either from the main bearings being shagged or the small-ends being oval. If the gudgeon pin holes have elongated in the head then inertia could cause the pistons to move more than they should whilst flying up and down. This won't be noticeable when turning by hand because you need the speed to make them come proud of the block mating surface.
4) Check behind the valves. If some of the valve seats have broken up and dropped inside this could happen???
Can't really think of much else...
My exhaust valves were all sandy coloured and my inlets were black when I did mine, dunno why, they just were...
Rover 3.5 V8 landy - Completely rebuilt and purring... Now awaiting a good tune!!