Do not fill it with any cement filler
As far as piston to cylinder wall clearances I would have the block rehoned on the cylinders needing it to remove the damages and have those pistons coated, in fact I would probably have them hone all the cylinders and rering it and have the pistons needing coating done
My reasoning on not filling blocks is you end up with two different temperatures zones in the cylinders that are less than completely filled, saw that with a 340 block half filled that the filled area was 180 F and the upper non filled part was 130F when dyno testing