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.
1999 Techno Violet Metallic BMW M3
2005 Audi B6 S4 quattro 6MT
2004 BMW 330i
1986 BMW 535i