Hi there and welcome to the forums!
It's great to have you with us and to hear that you've taken in little Kiwi.
We hope to see pictures of your gorgeous boy soon!
I don't know about the three containers in his cage, personally I think that's a good arrangement because you can feed him a variety of things, like pellets in one, seed in one, and veggies in the other, or something similar.
I would leave the water bottle and at least one of the troughs in there at first, she may not have seen him drinking and assumed he wasn't.
Spraying a budgie as their source of water is not a common practice, and it's hard to ensure that he's taking in any liquid. As long as you change all his water daily, there should be no reason he can't have multiple water sources. As long as he doesn't mind the spraying, though, it's a great way to give him a bath!
About the windows: Cage hear a window is fine, but right next to it wouldn't be good because glass absorbs heat and cold and even if there's no drafts, it still impacts the immediate environment around the window.
I hope this helps, I'm looking forward to seeing you and Kiwi around the forums!