My advice: remove all rock from pond edge (we call the rocks on the edge the coping stones). Using a shovel, rake, whatever, make the pond's top edge FLAT and LEVEL. Use a string level to make sure all areas of the edge are even with each other (to avoid low spots which = leaks). Make sure your liner sits on your new flat pond edge.

Large rocks tend to work best as coping stones as they are more stable than the light ones that you have now. Not sure what state you are in, but some sort of Amish Field Stone works very well as a coping. When properly shimmed, the larger pieces are very stable and attractive. They are also thick enough so you would use only ONE layer of stone on the pond's edge.

The easiest fix for your filter is to mound some soil around it, gently sloping away into the rest of the yard. Leave a shelf of soil around rim of filter (before you begin sloping it) to allow for coping on the filter's edge to better disguise it.