Awesome. I would love to read that!
Let me just see if I can add a few little extra points to your research, to help your Japan seem more real.
1. Know your season.
Seasons are very culturally important in Japan. There are festivals that take place in different seasons. Personal letters almost always refer to the season and the weather associated with it. Certain kinds of poetic imagery go with different seasons, and each season has different flowers and weather phenomena that are used to describe the moods associated with it. Even the patterns and appearance of dishes can be seasonally linked (my husband and I were once informed that we were using our fall dishes at the wrong time of year, not that we have ever stopped doing so!). There are certain dishes, or flower arrangements, etc. that are seasonal. Early spring is plum blossoms and icy weather, spring is cherry blossoms (ephemerality) and blossom-viewing parties; the rainy season is moldy and constantly drippy; summer is hot humidity and cicadas singing; fall is icy weather, red maple leaves and yellow gingko leaves; winter is cold and rainy or snowy, and New Year's celebrations and Adult's Day, etc.
Now, you don't necessarily have to research every last thing that goes with a particular season! However, knowing the season and the weather and natural phenomena associated with it will take you a long way toward having a cultural Japanese "feel" in your story.
2. Know your appellations.
You probably already know about the use of -san after someone's name. That is a pretty standard formal way for people to address one another, and it can be used after first names or last names. For boys, the suffix -kun is often used in the place of -san. Doctors, dentists, professors, or teachers should be called by last name with the suffix -sensei, as should artists. If two people have a very close relationship, things are a bit different. You can use -chan for either boys or girls, even among adults if the relationship is close and playful. Either -kun or -chan can be added to abbreviated versions of the person's name; we met a man this summer who went by "Yattchan" within the family (his full name was Yasuo).
When you don't know the name
Where we in English would use "sir" or "miss" or "ma'am," in Japanese they often use family terms that depend on the person's age and gender. These can use -chan instead if you are claiming intimacy (either in a playful or rude way).
Ojo-san = little girl
Onee-san = big sister, for a girl or young woman
Oba-san = aunt, for a grown woman up to middle age
Obaa-san = grandmother, for an old woman
Boku = "I", can be used to address a little boy
Oni-san = big brother, for a boy or young man
Oji-san = uncle, for a grown man up to middle age
Ojii-san = grandfather, for an old man
Sensei can be used all by itself if you know the person is a doctor/dentist/teacher/etc. but you don't know his/her name.
*Anata literally means "you," but in practice it means "darling." Don't have people call each other "you" unless they are boyfriend and girlfriend, or they are married.
3. Know where to use names, and where not to use them.
In English we have a habit of adding names onto the things we say. "Hello, George." "Well, your majesty, I have something to say about that." "Yes, sir." "Goodbye, Ms. Walsh." In Japanese, this does not work. Japanese is a language which allows for sentence subjects to be dropped - that means not only is no name used, but no pronoun is used either. I don't suggest dropping pronouns in English, ever, but in Japanese, people are not going to add names onto the end of phrases like this. Avoid it.
If you are going to put someone's name in - because you can - it will come before the utterance. So instead of "Hello, Yuko," in Japanese it would be, "Yuko-san, ohayo gozaimasu." The name comes first.
4. Know your "set phrases."
In Japanese, there are phrases that are expected to be used in different contexts. These are pretty much fixed, and they are not expected to be varied. There are a lot of them, and they don't always correspond directly to the phrases that would be used in English language contexts. Here are some important ones:
- ohayo gozaimasu - good morning. Do not use after about 10:30am, because it literally means, "It's early!"
- konnichi wa - hello. Use during the day after "ohayo" has expired.
- konban wa - good evening. Use in later parts of the day
- moshi moshi - hello. Use this on the telephone. It means, "speak," and can also be used any time you can't hear someone else, like "are you there?"
- mata ne/ ja ne - goodbye. This is a very informal thing said between friends who expect to see each other again soon.
- sayonara - goodbye. This is a very formal thing said between people who do not expect to see each other again soon, much like "farewell."
- bai bai - goodbye. Say this on the telephone, and only in modern times.
- dozo - go ahead. Say this when you are giving something to someone, or letting them do something.
- dozo oagari kudasai - please come in. Use it when welcoming someone as a guest into your house. Literally means "go ahead, please come up."
- gomen kudasai - hello. This is what you say when you arrive in a place (either home or business) but can't see anyone there, and would like to get some help.
- gomen nasai - sorry. This is what you say when you bump into someone.
- sumimasen - excuse me. You can say this if you bump into someone, or if you want someone's attention, or if you are apologizing.
- shitsurei shimashita - sorry. Literally, "I did something rude." This is what you say when you have either done or said anything rude. It's much more formal and more broadly applicable than gomen nasai, and more formal than sumimasen.
- shitsurei shimasu - literally, "I'm going to be rude." This is what you say after someone invites you to come into their house with oagari kudasai, as you step up into the inner part of the house. You can also say it instead of gomen kudasai.
- kudasai - please. Watch out, because this means either "give me" or "do me the favor of...". It can't be used in as many contexts as English "sorry."
- onegai shimasu - please. This one literally means "I make a request," and so it can be used in more contexts than kudasai. It can also be used in one context where in English we would use "thank you." If someone offers to do something nice for you, or to give you something nice, you do not say thank you in Japanese, you respond with onegai shimasu.
- omatase shimashita - I kept you waiting. Say this when you rejoin a group after stepping away, or if you are late to meet someone. People in stores will say this when they turn to you after serving the person ahead of you.
- chotto matte kudasai - please wait a minute. This is the casual form. The formal form used by storekeepers is "shosho omachi kudasai."
- tadaima - what a person says when they arrive home. Literally means "just now."
- okaeri nasai - what a person at home says when they hear an arriving person say tadaima.
- itte kimasu - what a person says when leaving home but planning to come back soon. Literally, "I'm going and coming."
- itte rasshai - what a person at home says in response to itte kimasu.
- osaki deshita - Literally, "I was before you," what you might say to others in your family after you preceded them into the bath. Possibly, what you might say to people waiting in line for a single bathroom after you come out and vacate the room for them.
- hai - This is often used for "yes," but can also mean, "I'm with you," indicating understanding rather than agreement. In the understanding sense, hai is often followed by...
- wakarimashita - Literally means "I understood"or "I got it." Often used when someone indicates that they have received a message and internalized it.
- kashikomarimashita - This is a lot like wakarimashita, except it is super formal, and often used by shopkeepers or other people to indicate that they have received a client's orders and will carry them out.
- arigato - thank you. As I mentioned, not to be used in response to a generous offer (in that case, use onegai shimasu). This is very useful in giving thanks for various kinds of generosity, and comes in many different forms. Domo, domo arigato, arigato gozaimasu, domo arigato gozaimasu... each one has the same underlying meaning but a level of formality roughly indicated by its length. The longer, the more formal.
- doitashimashite - you're welcome. Use this in response to thanks, but it can sometimes also be used in response to compliments.
- moshiwake gozaimasen - I'm sorry. This is a much more serious form of I'm sorry than any of the ones above, and literally means "I have no excuse." I've put it in the formal form, but it can also be used less formally as moshiwake arimasen or even less formally as moshiwake nai.
- itadakimasu - I humbly receive. This is what you say when you are about to start eating. Sometimes accompanied by a clap of the hands into prayer position. It expresses gratitude toward the person who made the food, and is usually answered with "dozo."
- gochisosama deshita - It was a feast/treat. This is what you say when you have finished eating, or when you are about to leave a restaurant (if you feel comfortable speaking to the proprietor). It is also used to tease people engaging in public displays of affection, as if a public kiss were a rich dessert.
- irasshaimase - This is the welcome that people running a restaurant will cry out, aloud, to people who enter.
- baka - this is not a set phrase! It's a very rude insult that is much more rude than our word "stupid." You can use it by itself, or as baka yaro (also extremely rude). However, if you want to say "stupid X" you have to add "na." This is something I see people miss a lot. So you could call Taro-kun "baka," but if you want to say "stupid Taro," it would be "Baka na Taro-kun!"
This turned into a long list! However, I'm not sure I covered everything. So if you have additions or questions, feel free to put them in the comments. Have fun with your story in Japan!