Okay, so this is just a partial list of things that were off. Putting the wall of text under tags so as not to flood everyone who may not want to read all of it.
Summary
The Shinto kamisama names must always be spelled respectfully.
With the exceptions of Izanami and Izanagi accompanied by “No Mikoto” since they were creators, all the other kamisama are referred to by their names along with “Omikami”
“Inari Omikami” “Amaterasu Omikami” etc etc. (There may be specific exceptions, but it’s considered okay if the omikami title is simply use, if in doubt)
Not referring to them like that, it’s considered a sign of deep disrespect inside the country.
Shinkansen scene:
Calling the protagonist “Rei-Kun” is wrong. Not only it should be written as “Reikun” or “Rei-kun” but using that honorific is not suitable for the situation.
For starters only high schoolers or people with truly deep relationships, would refer to each other as “-kun”. Keep in mind that Japanese are not as extrovert as other cultures, so for two Japanese to have a deep relationship, they would have to spent a lot of time together, and know a lot about each other. This doesn’t seem to be the case (at the moment)
Keep in mind too, that “-kun” is usually used for males, while “-chan” is usually used for children and females (which was done right).
The only situation in which maybe “kun” would be used between too adults, would be if they were work colleges, and one party was the senior of the other party. But we would be talking about a huge age gap. Like one person being 50 years and the other 25, for explaining it properly.
In this case I think it would be better for “Kage” to either refer the MC as “Rei” or if Kage wants to be polite “Rei-san”
About the ticket scene (side note, I would dismiss it for creative reasons, but my friend is Japanese and she is not, so it made the list anyway). Her suggested: it would be interesting to make some pointers. Japan doesn’t use paper tickets anymore; they use electronic cards or their phones directly. Keep in mind too, that Japan is a truly polite country, and for accuracy, it would be considered deeply rude to ask a passenger for the ticket. There’s also no need, since the shinkansen access gates are always guarded, so you must have a ticket when boarding the train.
A suggestion, if you want to introduce the MC name there’s a more accurate way to doing. Long distance bullet trains, usually offer bento or snacks to their passengers, and the payment is usually done using an electronic card or more commonly a SUICA card. So the MC could be paying using that method (And even if SUICA cards doesn’t have the titular name on them) you could take the creative liberty of saying the name is on the card. This way you get the same effect, and make the whole thing more accurate.
Another thing that I believe could be changed, because it feels weird, is two Japanese men talking about how something is said in English. So instead of saying “Its called Bullet train in English for a reason” since they are Japanese, it would be fitting and pretty original to make a joke referring the Kanji “新幹線”Shinkansen, And say something along the lines of “It has the Kanji for high speed line after all” or something of the sort. It will make the conversation feel more genuine.
When we get to choose or specialty, I went for the Katana specialty. But I think you should change the “My classmates called me the Samurai” because a Japanese person, would never use that as a nickname for a kendo practitioner, since Samurai would refer more to a social status or nobility. Instead you could use something like I was called “The second coming of Musashi” or I was called “The incarnation of Muramasa” those sounds dramatic, but more accurate.
About the katana training, I will give some pointers to make it more realistic an accurate. Kendo practitioner start with “bamboo” sticks, not blades, but there are different kinds. First is there the “shinai” that is the lighter one, and for beginners. Then he could move to using Bokken (Actual Bamboo blade) that is more close to the katana in weight and is good to train. Then move to Katana. It would be advisable for the MC to have been practicing since he was a child (not weird) so it would make sense for the MC to have a certain grade of mastery when it comes to use a Katana. Keep in mind, that you cannot bring a katana with you in modern Japan, unless you hide it. Police would stop you.
About the names:
You let the player choose “traditional names” but mostly of those are not traditional at all, and some of them are not even considered names.
If you are trying to be accurate, you must not use “kira kira” names, like “Yami” for example. Keep in in mind, that names are really important in Japan, since parents tend to name their children regarding to what they want for them. If you want a strong boy you will use the strong kanji, kind the kind like kanji. It goes to the point, that when you go to register your baby’s name, the civil servant could negate your name if they believe the name is not appropriate. If you try to call your child “lord of the night” or “pure darkness” those may not be seen as appropriate.
This online list, come with the kanji and the meaning easy to understand:
100 Japanese Baby Names: Meanings & Origins
But in case you would want to make your own names, in a truly traditional way I would recommend the following tip:
Traditional mal names tend to end with-maru most of the time, because it’s a particle referring to “the strength of a man”. So you use the adjective you want and add “maru”
Now with female names, it’s the same formula, but instead you use the “ko” Kanji, who refers to “girl”. Then you use the adjective you want. Its very normal to use “flower” like adjectives or names along with the “ko”.
A lot of names in Japanese are gender neutral, with the exception of the ones with a obvious “gender” meaning.
I know there are some creative liberties that are necessary for story, but these are some things for societal accuracy that really felt off.