Serious water spot removal

I just purchased a new vehicle in perfect mechanical condition, however the jackass that owned it before me let it get doused by a sprinkler over quite a period of time. The result; water spots over a good portion of the car that are not going to come off without a lot of persuasion. I took it to a local auto detaililer and they stated that an Acid wash would take care of the majority of the spots but there would most likley still be an faded outline of the water spots remaining on the vehicle. They stated that claybar would not work on the spots.

Any ideas how I can remove these spots on my own? Once they are on is it pretty hard to get them off? There are also various scratches around the vehicle. What is the best way for removing these? Clay bar and wax?

Thanks