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It sounds like you need something a bit more aggressive than just ScratchX. If you were using a Meguiar's dark red pad that's our cutting pad. We don't always recommend that for use on a Porter Cable because it has a high probability of hazing the paint, but if it did not haze your paint, then don't worry about it. You might want to pick up some Ultimate Compound from Walmart, Advance Auto, etc and use it instead of the ScratchX. It's a definite step up but super easy to use, it won't scour the paint and should leave a very nice finish. Use the tool at speed 5 or even a bit higher, use a fair bit of pressure but keep the pad spinning, and work an area about 18" x 18" at a time, wiping off the residue as you go.
Just know that water spots can be crazy deep and extremely difficult to remove in worst case scenarios.
I just picked up a Chevy 05 SSR truck with 47K miles. It was stored outside in the Hot Florida Sun. I have tried to detail it and have one area that is giving me fits. The tondeau cover over the rear bed I belive is fiberglass and matches color (red) of the truck. There appears to be a bunch of what I think is water marks.
I washed it and clayed it. Then using Scratch X and my old Porter Cable. Don't recall the foam pad that I used however don't think it was the finishing one and it is a dark red color having a harder finish. I made several passes getting rid of some small scratches and some of the water marks. I then used Zaino polish/cleaner and then the glaze. The color looks better and from a few feet away it looks good. When it is under the florecent light in the garage is when you can pick up the water marks.