Are chopsticks used for all meals? Pretty much unless it's liquid and/or western foods.
Is it impolite to wear shoes inside? Impolite probably isn't even the right word, it's such a cultural standard to take off shoes upon entering the house that it would be really weird for someone not to. Sort of like going to bed wearing your wet coat.
Are kimonos still worn, and if so, in what situations? By average people? No, unless they want to dress up for some reason like a festival or an event that is highly traditional. People wearing kimonos daily are likely those owning small tea shops or other traditional business, Geisha, and the like. That's not to say that there are definitely different fashion trends in Japan.
What are the older generations like compared to younger generations? I'm not sure how to answer this one because this is really broad. The subject of family was brought up so I'll remark on that. Family is a big deal in Japan. They live an interdependent/interconnected lifestyle with the family. However, in modern times and with women gaining more control over their lives all over the world, family is taking a back burner for many Japanese youths. The reason being lack of adequate daycare facilities and women wanting more to secure their own futures over getting married. Since family is to integral to lifestyle, taking that leap is not an option for many young Japanese people, this has also lead to a decline in birth rates drastically for several years. If you're juxtapositioning the grandmother versus young girls, this is something to keep in mind.
Any information helps. I also don't have a Japanese town in mind yet. Maybe you have suggestions? I don't think you need a specific town, you can even make one up like we do in our western writing. I would suggest choosing what climate you want your story to take place in and accessibility to major cities, that will help you narrow it down so you can start looking at regional culture. I would suggest however, you try to stay in the Tokyo region if you want your story to appeal to a western audience since most if anything people know about Japan tends to be related to that area.
Another note, someone suggested watching anime, reading manga, watching popular shows from Japan to get an idea of the culture. I don't agree with this. Though manga/anime are much more prevalent in Japan than western societies (of course), picking any random title to indulge yourself in will not give you insight on "Japanese culture". It will give you insight into a subculture. Everybody in the states doesn't watch Big Brother, read Batman, and laugh at South Park. You just picking something random to watch will give you as much insight into the culture at large as picking those mentioned titles would to a Japanese person about American culture. Furthermore, anime/manga though viewed by a much wider demographic than in western countries, is still only majorly viewed by a subculture. To get a generalized view of the culture at large this way you would have to watch an outrageous amount of anime, spending a tedious amount of time doing that than just reading on the culture from google.
My MC in my manuscript is Japanese American and though I am FAAAAAR from an expert on the place, Japan has been immensely interesting to me for well over a decade. I agree with the poster that suggested narrowing down where your MC will be. As well, watch youtube videos about everyday life in Japan. They're the closest I've come to feeling like I'm there without being there.
Last note, I've read several books from Japanese authors and what I've noticed more than anything is that it's not so much what your character does that will make them authentic Japanese seeming, but how they think. I'd suggest going about your story as normal when you've got your bearings and then alter your scenes to "make-sense" for a Japanese person. But since your MC is Japanese American I'd wager her misunderstanding of others mindsets would more be the issue. Japanese people are not very direct and avoid conflict. The very structure of the language highlights this as opposed to English more emphasis is laid on the subject than the action. Example: Western - Someone broke the vase Japanese - The vase was broken. It's an incredibly interesting subject I've studied on in a couple of courses, but I digress. As a teen girl, your MC will likely be around other teen girls in Japan where cute is everything, high-pitched voices, the V sign, mobile phones for days, basic teenager stuff. Bolder Japanese girls like to stand out a bit by coloring and cutting their hair (but don't go full anime). The main thing you're going to need to read up on is the school system however. It's much different than in Western countries and going to be WAY different in a rural setting.
Hope I helped at all.