This is mainly a copy/paste of notes that I prepped for a friend back in 2015, with updates now and then.
Part 1: General stuff
Takuhaibin (aka kuroneko) offers a relatively cheap service of sending your luggage ahead. You can send it to specific addresses, and have it arrive on specific days, specific times! Very handy for doing side tours. Ask your hotel or nearby 7-11 for help arraging it.
There is often no soap in public restrooms. You may want to bring hand-antiseptic.
Often people speak surprisingly little English. Keep that in mind when booking stuff (better to ask hotel lobby to book stuff for you rather than just showing up).
use hyperdia to check train schedules. NOTE! With the JR pass you can't use the Nozomi/Mizuho/Hayabusa shinkansen, so uncheck that option! Hyperdia has been discontinued :(
mini-souvenirs! Giving little gifts is a huge thing in Japan, and it's very convenient to have mini-souvenirs to give back (especially when people go waaay out of their way to help you, which happens more often than you might expect). My recommendations are these 25g ragusa: cheap, blocky (don't break) and small enough to carry around. Might melt in summer though...
Untangling my Chopsticks is a nice, relatively short read if you want to get an idea of the culture beforehand (focused on kyoto and food). I would recommend getting a physical book and not kindle though, since at the end of many chapters are recipes.
Go to at least one onsen! Onsen is a hot-spring bath (usually public but sex-segregated)Sentos are also super nice! (almost same as onsen, but the water isn't from a natural hot spring). Especially in the south, sentos are often still part of people's daily routine, and quite an experience.