Josh and Ninety,
Try these techniques, in order, on the water spots. If one works don't move on in the list. If it doesn't move on.
1. Try a 1:1 mix of white vinegar and water. It's best to apply the mix to a cloth or sponge and then apply it to the glass... it takes care of any wax on any paint it might touch and may discolor paint depending on the paint's condition. A microfiber cloth works best and even better is one of those Mr. Clean magic eraser things. Rinse the glass and surrounding areas completely and dry the glass immediately with a microfiber towel or cloth.
2. Try white vinegar with no dilution. It's best to apply the mix to a cloth or sponge and then apply it to the glass... it takes care of all wax on any paint it might touch and will likely discolor paint depending on the paint's condition. A microfiber cloth works best and even better is one of those Mr. Clean magic eraser things. Rinse the glass and surrounding areas completely and dry it immediately with a microfiber towel or cloth.
3. Go to an appliance store or somewhere that sells appliances and get some glass cooktop cleaner... it's a white lotion looking stuff with micro-abrasives. Go get one of those dishwashing sponges with the blue scotchbrite on one side. Apply to cleaner to the scotchbrite side and gently scrub the glass... kinda like applying wax. Then you can wipe or rinse it off the glass. Be careful about getting the cleaner on your black weather seals. It's alot like getting wax on the rubber. As an alternative, Brasso and/or Mother's Aluminum Polish should work too.
4. If those don't work, let me know, I've got another trick but you'll need to be a bit more careful and precise as it includes the use of diluted muriatic acid.