I did some research and discovered vinegar and water works to remove hard water stains. I laid a towel soaked with 50/50 water/vinegar on the problem area for 7 minutes to let it fully penetrate. Afterwords, I dried the area and hit it with scratch x two more times. No more spots. After that I threw 2 coats of P21S hard wax over the whole area and it looks great.
Past: 1999 Techno Violet Metallic M3
Present: 2011 135i 6MT