low O2 will definitely cause a ph drop that why ph drops at night when the lights are off and is combated with a reverse cycle fug. I agree cloudiness was probably a bacteria bloom from the new rock and your possible paly/zoa getting covered. Small tanks are so unforgiving on parameters you probably could have got by with what you did on a bigger system. If you are having ph problems after you get this sorted out the best this to do is build a small CO2 scrubber for the air intake on your skimmer the mod is usually good for between a raise of .1 to .3 in ph for now best thing is surface agitation. +1 leave the skeletons for awhile you might get lucky