I'd recommend a fine compound or paint cleaner to cut into the clear a bit to remove the water spots if nothing has worked yet. If you aren't familiar with how to use the products, I'd have a pro take care of the areas that are affected. It is tough to get swirls out of black if you get them in their really bad.

It is likely acid rain or something harsh in the water that sat on the car before you bought it. Bird crap will do the same thing.

When I worked at a local body shop, we had to re-paint a lot of brand new cars due to Bird crap, rail dust (from train transport), or acid rain. Some of it would cut all the way down to the etching primer. These were Ford products that were built less than 2 months prior, and the paint was eaten away that quickly. Pretty amazing. I will give them credit though - Ford did disclose the info and discounted them nicely.