You can get any concrete cleaner at home depot and just wash the stone with a hard broom.

That usually gets rid of cement stains as well as rust or moss on the stone.

If that does not work, I would recommend changing the damaged stones. Painting is NEVER a good idea on stone...

Let me know if you need more info.

My dad has used oil-based stains to change the unfortunate mismatching on a few stones at his house, and they look fantastic. He buys little cans of stain and blends them with rags. There are some concrete stains available too, but I believe they are very expensive.

Renee