I heart all of this so much, I can't even begin! I love both Chicago and San Diego, gorgeous cities and I can really see these two being home to Nat and Clint. They truly play to both their characters, Chicago is beautiful, seems a bit harsh and cold at first glance yet captures you with its soul once you see beyond the shiny glass facades. And San Diego is so homely, earthy and airy at the same time, I totally accept your headcanon regarding these cities :D

I would love to read about Tokyo, I can totally see Clint being a geek about the windcurrents ;)

Also, your AU/Alternate Backstory sounds really intriguing!