I would take those rocks out and soak them in scalding hot water with a dark blue solution methylene in a bucket over night, maybe for two days, just dump the water down the toilet and fill it up with hot water and M. Blue again, then take them out and put them outside to air out for a day or two, those things are very stubborn to get clean. Hell i suppose you could use bleach too as long as you rinsed them off like hell before putting the back in the tank.
As far as the cories are cocerned, idk if you have a hospital tank yet, but it might be worth the money if your dedicated enough to the fish hobby to get a ten gallon tank or plastic Tub to use as a hospital tank, you seem to be having alot of problems, now that the rocks are clean, you could dose just a little Methylene to the main tank and still maintain a Decent supply of Benificial bacteria. Maybe not more than half strength. One time just to kill some of the free floating microbe spores.
Edit: But be careful, it will stain your sand its the best thing you can do for the tank, 2-3 ML per ten gallons of tank at least once, but you may have to stir and remove the top layer of sand, but its the best anti-microbal anti-fungal chemical dye on the market today, scientist use it to clean their glass culture jars and such.