""How did the pre Inca remove the organic skeletal remains from the quarry limestone and add microcrystals to the reconstituted mix? And why? "
Ya its cryptic to just answer with questions, but you must have good reason for it.
Ok, I'll give it a shot. What are those organic skeletal remains? Mostly shells? And while the original material was probably full of all kinds of organic material, the shells happen to have a durable enough makeup to remain the last man standing during the process of fossilization and turn into calcite or silica. So its really calcite or silica which has left the impression of that original organic shell piece, but not actually a shell.
So if you have a magic material science tech that has figured out how to loosen the bonds of material, then it goes without saying that in that moment of loosening, those shell 'impressions' will disintegrate as the material expands into a looser slurry or Plasticine state. Its not like crunching up the rock to leave particles of preserved shell fragments. Magic material bond loosening would be evenly distributed at the molecular level so no tiny shapes would survive. And nothing was removed really.
I'm being recklessly loose with my invoking here to be the lightning rod of ridicule so you might be able to more clearly explain your position behind the shadow of my giant distraction WOO.