Sorry to here about that issue of well water and spots on your new truck, I would be so pissed. I have always used Zaino Brothers polish on my cars and trucks, love this stuff, real amazing products.
The first thing I did when I got my truck was 2 coats of Zaino brothers polymer polish.
you can find there products here and what they do.
I usually put 6 coats every 6 months, but since it was still winter here, I could only put 2. Will be doing a full clay and zaino next week when it warms up a bit.
you might want to look at this product, on my old grand cherokee I has some spots like you explain, not sure its the same thing, I had tried all sort of paint cleaners and clay bars, never got rid of them, but I used this product on it and it got I would say 85% gone, you can barely see them. Might be worth of shot, many of there products work really well for dark colored paints.
Z-PC Fusion Dual Action Paint Cleaner Swirl Remover
Hope this can help