Money
You will need quite a lot of cash, especially in restaurants. There are plenty of ATMs in Japan, you’re never too far from one in cities. Bank ATMs don’t have fees until late evening, convenience stores have like a 2$ fee. But the biggest fees are by your home bank, therefore I use a Revolut card for travel and zero ATM and exchange fees.
Language
English proficiency in Japan is low (ranked 87th among 113 countries by EF English Proficiency Index). Most young people have an understanding of English but are unlikely to be able (or willing?) to speak it. Touristy areas have slightly more English, but still one cannot fully rely on English anywhere. Useful to learn several basic Japanese phrases. Google Translate camera is useful to translate menus and signs. However, all train stations have signs in English so it is easy to go around.
Navigation
Navigation works completely fine with Google Maps only – 99% of train and bus schedules are integrated into the app, no real need to use dedicated apps.
Taxis
Uber works in Tokyo, but the usual way to get a taxi is just hailing it on the street. Taxis are relatively expensive, but for 2+ people in some cases might be cheaper and way more convenient if you need to take a local bus somewhere or multiple transfers are required or you are in a hurry. Uber is paid in the app and most taxis take cards now.
Onsen
Go to onsen (hot springs) when you can. It’s gender-seperated and in the nude. Many traditional hotels (ryokan) have them. At least one night in a nice old ryokan is a must when visiting Japan I think. Onsen towns (Beppu, Kusatsu, Hakone, Nozawa, etc) are cool, while some might have little else than onsens. I love natural outside onsens, but these are mostly quite hard to access. Tattoos are generally not allowed, but there are some exceptions. Small tattoos can be hidden with an adhesive bandage or something. Follow the rules: https://www.kashiwaya.org/e/magazine/onsen/rules2.html
Restaurants
Japan is foodies’ heaven, in my experience (50+ countries) it has the best food in the world.
Try different types of restaurants, there are many: https://www.japan-guide.com/e/e2036.html
Look for restaurants on Google Maps, maybe TripAdvisor (more foreign reviews). If you want what the Japanese like, use local website/app Tabelog. Just note that Japanese are really strict about rating restaurants, so 3* would be quite good and 4* is approaching Michelin-level, 5* practically does not exist.
Most good restaurants require reservations for dinner. Some have TableCheck reservations or reservations via Tabelog. But the vast majority reserve by phone only, usually in Japanese. Hotels might be able to reserve for you sometimes.
No tips!
There’s no tipping in Japan. If you leave change, servers will think you forgot it. Some might find it rude. I have seen some foreign tour companies asking tips for guides, but that is just a way to get more money and totally not done in Japan.
Avoid busy spots
Many tourists started pouring into Japan again, so touristic places are very busy (esp. Kyoto and Tokyo). It is especially true during sakura and koyo (autumn leaves) seasons and big Japanese holidays – Golden Week and Obon. To avoid the crowds, go to tourist places very early or late (if they are open). If you get too annoyed, try more remote and not as popular places.
Hiking
Go hiking. Prime regions in Japan for that are North Alps (access via Kamikochi), Tateyama (via Toyama through Murodo), South Alps (somewhat of a hassle to access, via Nirasaki), Yatsugatake (via Fujimi). These are 2500-3000 meter peaks, they get heavy snow, so easily accessible mostly May-October. Closest nice mountain near Tokyo I think is Tanigawa (very well connected with Shinkansen and ropeway, while expensive). Plenty of great mountains in Kyushu island (Aso, Kuju, Kirishima). Tohoku region is not as visited by foreigners and takes time without a car, but many great peaks like Iwate, Bandai, Adatara, Zao.
If you have time (at least 4 days), ancient pilgrimage routes (Kumano Kodo or Henro) are cool, it’s more of a rural hike than a religious thing for foreigners. It is a good option if you don’t want big mountains and good for early spring/late autumn when the mountains are tricky. Summertime is too hot in these areas. The infrastructure is very good and plenty info online.
Cycling trips
Cycling around Shikoku island was one of my favorite things in Japan. Most people do only Shimanami Kaido route, which is beautiful and easy, takes 2-3 days. Rentals available. Plenty other great routes in Japan.