I know lots of people disagree with this, but removing the water movement is contrary to the desired result. Moving water loses it's sediment load quicker than still water. If you turn of the PH, you'll likely see another clouding when you turn it back on, since the sediment that does settle out will do so in areas that are high flow. Keep the water moving, and it will settle out.
In the future, you may want to use a turkey baster or small line of tubing to siphon the loose detritus off of your rock prior to moving it around to minimize clouding.