If you’re going to Nagato via Shinkansen, I assume you’ll be getting a JR pass? Because if you aren’t, you really should! I’m honestly not familiar with Nagato nor Kami (is that the same Kami in Saitama), but I would highly recommend going to Kyoto to visit Fushimi Inari or Kiyomizu Dera. Since you’ll be in Nara, it’s just an hour away from Kyoto!
Tokyo is a very bustling metropolis, and there are so many places you can visit. Aside from the usual Akihabara, Ikebukuro is a nice place as well, and it has an Aquarium and Planetarium~ You can also go to Tokyo Sky Tree and get a good view of the city (and they also have a planetarium and aquarium lol). Since you’re there during the hanami season, you can go ahead and visit many of the numerous parks there. The rest of Tokyo is all heavily dependent on your interests. Harajuku for fashion, Shibuya for music, Shinuku for nightlife, and so on.
As for not how to crash and burn, well… You can generally play the gaijin card and people won’t look down on you so much Most of the things that they put on the internet is true, though. Don’t be noisy on trains, don’t litter, don’t stand in the middle of the road, etc etc etc. The bottom line is; be very self-aware and considerate. There is no such thing as “oh it’s just a little thing, people won’t mind” in Japan. They do mind, and it helps to be aware.
The trains are also mighty confusing! Even if you use an app like hyperdia, and you know what line you should take, there are two directions that that line goes and you may not know which direction is the right one and which platform that direction is on. Don’t hesitate to look up a station list so that you know which direction the station you are going to is in. Usually they mark directions using the end stations of the line, so look up what the end stations of that line are.
One thing to note is the language. A lot of people say it helps to learn a few basic phrases when going to Japan but, to be honest, any of those basic phrases that one would learn, most Japanese people already know in english anyway. So if you say “sumimasen” or you say “excuse me” they will know the difference. What WOULD be helpful to learn are kanji that you can find in signs. Kanji for station, left, right, up, down, floor, numbers, yen… stuff like that.
Other than that, enjoy! I’d say make sure to appreciate more than just the anime, but the fact that you are going to places such as those means that you already plan to do so XD