As a last resort, you could take the car to a quality body shop for an evaluation. One thing they might do that I wouldn't advise doing at home unless you are a good paint guy, is color sand the affected areas of the car using something like 2000 grit wet or dry sandpaper.

 

that is WAY over kill and I will guarantee is NOT needed for water spot etching.

 

It turns out the water spots weren't etched in. I went out this morning to clean the car before it got to hot, and I used some hard elbow grease to remove some up the spots in one section before I got to hot and gave up. So I'm sure when the weather cools down and I give it a clar bar cleaning it should fine.

Thanks for all replys, this forum is the best.