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By the way, thanks for the is new information! I've never used more than window cleaner on my windows.
+1 to the questions - I assume you don't need the vinegar step if you've clayed. But as for "waxing the windows" - is this plain-old finishing wax? What about the Rain-X glass treatment stuff - does that work as well or better?
I've always struggled with water spots. Idk if where I live we get super acid raid or what but they're pretty bad and hard to get rid off from paint or glass. I've tried vinegar, alcohol, acetone (on glass), and even gas. Gas actually kinda works and doesn't damage the paint if you're careful but still dangerous and makes you question your decision. I did finally find something that works quite well on glass (and even paint with the right mixture ratio). I had pretty bad water spots on the windshield on my 2015 GT. They were basically everywhere where the wipers don't reach. I tried all the above mentioned chemicals to remove them to no avail. Then one day it occurred to me to try this acidic pantoon cleaner which does magic on anything aluminum and Bingo! (I use it to clean anything aluminum around the car like brake calipers, engine block, etc.) Works like magic. No need for any scratch pads or abrasives or waxing or claying. Just spray some on the towel (I used microfiber) and rub it into the spots on the glass and they come off quite easily. Now of course it depends also on how you mixed the cleaner. It comes concentrated and you mix it with water based on your needs. You have to play with the ratio until you get what works for you. I think mine was approximately 4 to 1 but I don't recall exactly. CAUTION! This stuff can be dangerous, it's a really strong acid. Wear protection!
I bought this solution from a local place that makes it here in the Upstate SC but I'm sure there are others that make the same. It's Wampole's Pantoon Cleaner / Aluminim Cleaner Brightener.