Japan is easy to move through once you have a working phone and an IC card, and confusing for about two hours at the airport if you have neither. Trains run on time. Stations are marked well if you can read the Roman letters, and better if you can match kanji. Tokyo and Osaka are huge and walkable at neighbourhood scale. Kyoto is the city people add because of temples, and it fills up. The countryside and the north are a different density.
The shinkansen is the spine between the main islands’ big cities. Local trains, subways and buses fill everything else. An IC card (Suica, Pasmo, ICOCA and the others, now largely interchangeable) pays for most urban transit. Cash is still used in small restaurants and some rural counters even though cards have spread in the cities. Japanese is the language of daily life. English exists on major transit and in hotels; it is not how a neighbourhood shop runs.
Take shoes off when you are asked. Stand on the correct side of the escalator for the city you are in. Convenience stores are a genuine part of how the country feeds itself at odd hours. A first trip usually means Tokyo plus one other region: Kansai, or the mountains, or Hokkaido in season. Trying to see the whole archipelago in ten days is how you live in stations.
