I have used the scratch x as well. Alone it took off most of the spots but there were a few that were still there. I used dish soap to wash the entire car, doing this removes all the wax and other things you may have used in the past. Once I did that I tackled the trouble spots with a 50/50 distiled water and vintager solution. That lightened them up pretty well but you could see the outline of a few still. Then I went at it with the scratch x again being sure to take my time. That did the trick, no more water stains and a freshly waxed car.
I had tried clay bar as well with no luck. I was really concerned that the spots were etching at that point. It took some doing and elbow grease but the method I used worked. Hopefully yours are not as bad as mine. My car got hit by some sprinklers while I was working in a hotel on Miami. It was in valet parking so I had no idea till I got it back 5 days after I arrived... This was easily the worst I had ever seen water spots so you may not need to go as crazy as I did but if you do, this should do the trick.