maybe some one can correct me if i am wrong, but for the rocks without coral, couldnt OP put them in a dark tub for a few weeks to kill off all the pests? BRS calls it "cooking" but has nothing to do in the kitchen. You get a plastic garbage can with a lid, add saltwater, a heater, and air pump and let the rocks sit like that for 2-8 weeks with water changes. That should clear up the rocks?
They can live without light it seems. They do fine in the dark areas of the sump, probably just catch food.