For the glass, I have a small (maybe 4oz) container of a cleaner called 'sparkle'. White container with blue writing, milky consistancy. I bought it from a window tint shop when I tinted the windows. Takes a bit of work but it got rid of the waterspots (my windows looked like yours). I followed up with rain-x.
My girlfriends Explorer had waterspots on the paint nearly as bad as yours. I spent HOURS with a claybar, and a bunch of different waxes, and got the worst of it off, but it takes forEVER. Take it to a detail shop and see if they can fix it, cause it takes way too long to make it worth it. I figured out how my girlfriends paint got that way, she let some kids wash her car at a fundraiser MONTHS ago, and I think they used dishwashing soap or something and it stripped the wax (I used to have a great coat on it). Then she parked it next to a sprinkler every night for about 2-3 months.
2006 F150 FX4 Super Crew - Bilstien 5100s leveled 2", 35" KM2s, 4.56 gears, Detroit locker, Eaton E-Locker, Traction Bars, AEM intake, Xcal 2
2010 VW Golf TDI 6MT