To be honest, there's a lot you can derive about Japan just from watching anime or reading manga. Though many aspects of it are probably stereotyped in some way, it is these stereotypes that makes it in the mainstream products. This eventually bends the audience to accept these stereotypes. That being said, you don't need to know a lot about a culture to understand it. Just observe, and you can get results.
The second thing I want to point out is your creative take. Down to the core, a story is what an author had imagined and created. There's a lot of room for differences between one and the next. The point of view of your protagonist (IE: Optimistic) also can heavily impact how scenes are portrayed.
If you are persistent to sticking true to reality, there's probably a handful of us that has been in or knows much about Japan. It's
very similar to the western world, and the Japanese makes great efforts in considering themselves westerners. However, like any country in the world, they have both urban and rural areas, as well as their own language and traditions. These things aren't exactly hard to identify, and if you need em in your story, chances are you can google them up.
I love your idea of the story. For all y'all who have watched Wonder Woman, I feel as if the character will be similar to Diana
(Good movie, watch it everyone). Best of luck, and choose whatever path is best for you.