I’m open to suggestions, especially since I haven’t actually been to Japan yet. Obviously, it can’t really be in an extremely urban area like the heart of Tokyo, as there wouldn’t be room for a property like where my character’s house is due to the size of the garden. Another consideration is that the location should be somewhere that doesn’t fall in to the area where the Kansai dialect family of Japanese are spoken, as my detail of “Due to her grandmother being from Kyoto, she slips in to speaking Kansai-ben at times” would be rendered moot. For a map of the distribution of dialects in Japan, look here. Lastly, looking at all the species of flowers I mention in my character post, the most ideal location looks to be a part of Japan that classifies as a hardiness zone 8. For a map of hardiness zones in Japan, look here. Given all of these factors, I’m thinking that possibly the best location would be somewhere in Ibaraki prefecture. Almost the entire prefecture classifies as zone 8, it is in the Kanto area, and is only slightly effected by the Greater Tokyo region (the Wikipedia article states the population is modestly increasing because of it).
Edit: Given that there are only two shrines of note in Ibaraki as far as I have been able to find, we should probably create a fictional town within the prefecture. The one shrine which looks as if it might have miko (anyone know for sure?) is Kashima shrine, and that looks to be in one of the few areas that isn’t hardiness zone 8.
Edit 2: On second thought, maybe we should just create our own little fictional island, like a few games I can think of off the top of my head.