Weirdly enough, I had some of the same ideas as you. I also thought that Nanashi's companions made up a specific part. Asahi was the sun (it's in her name and she brightens everything up), and Navarre was the wind (because as a ghost he couldn't make anything, just enhance or move things around), but the others were different. Isabeau was the earth because she's so grounded. Nozomi was plant life, because I associated Nozomi being motherly with plants providing food for animals. Toki was animal life, because at the start she does her own thing and is cold and hostile, but becomes one of the most loyal companions after she's treated with respect. Gaston was the oceans, because he takes your turn in combat. When you go sailing, you have to bow to the tides. Had Hallelujah been in the lineup, he would have been the seasons. Not just because of his fire-ice powers, but also because he's stronger than he seems.
Instead of Nanashi trying to heal Flynn, I thought that Flynn would try to kill him if he regained his mind. So in my story, Nanashi reincarnated him.
For some reason, this one seems more erotic than emotional than the others. That's not a bad thing; it just is. I also like how Nanashi tells Hallelujah that they can stop at any time.