Just back from Japan (as in, yesterday!). Went for two weeks with DH and DD (10). Here is some information I wanted to include that I haven't seen posted everywhere...
You don't need a tour company - save your money! Japan is insanely easy to navigate around and you don't need any specialist knowledge to book things or research activities. I'd also avoid Klook and similar services as you can very easily book your own tickets to things if you have a bit of patience navigating Japanese websites (Google Chrome will automatically translate the sites if they don't have an English option). Having someone book your tickets to attractions or the train is just a waste of money.
We flew in and out of Tokyo Narita. Two nights in Tokyo, five nights in Kyoto, two nights in Hiroshima and then five nights in Tokyo. This is a very "beginner" itinerary but was a good introduction for future trips. While the Shinkansen (bullet train) is fast and efficient (you can show up to the station five minutes before it leaves), the travel days are still draining due to the crowded stations and the humidity/heat (less of an issue in April, I imagine?).
Japan has embraced credit cards (they didn't prior to the pandemic) but the transit system and some smaller restaurants and shops are cash only. 7/11 ATMs can be used with your bank card for withdrawals.
Highly recommend keeping a list of things you'd like to do versus having an hour by hour, or even day by day, itinerary. You won't get to everything on your list and that's perfectly fine - half the pleasure is just strolling around and immersing yourself in Japanese life. Sometimes places are more crowded that expected or not as interesting as they are hyped up to be so being flexible is key.
The metro in major cities is easy to use - just input your destination into Google Maps and it will tell you the fare, the platforms to take and the exits to take. That information is very helpful as without it, you can easily get lost in the stations as they are large and confusing.
The Japanese are incredibly friendly. Please, for the love of God, learn how to say "hello", "thank you" and "goodbye" in Japanese. It's common courtesy and goes a long way - people appreciate the effort and it's thoughtful as even as a foreigner, you are served in Japanese as many will not attempt English out of fear of not speaking it well.
We stayed in hotels the entire trip. Highly recommend finding hotels that offer breakfast as it's quite hard to find restaurants or cafes open before 10 a.m. in Japan. People rave about 7/11 food but it's a bit boring to have every day for breakfast. Breakfast places are expensive and full of tourists, anyways.
Eating out is quite cheap. Many nicer restaurants take reservations by phone - ask the hotel staff to do this for you. You can also show up when they open and arrange a reservation for the next day (we did this a few times just randomly walking by places). Restaurant food is cheap and flavourful. We downloaded the Google Translate app and would use that to interpret menus in real time. It's needed - a lot of places offer things like horse meat so you'll want to know what you are ordering.
Japanese people are very mindful of public behaviour. They speak softly in public spaces and are mindful of things like which direction to walk on the pavement. We tried to emulate this as they have to deal with a lot of tourists as they navigate everyday life. Be especially mindful at shrines and temples, especially the less popular ones. People are coming for spiritual engagement, prayer and meditation and a tourist taking selfies or having loud conversations really ruins the vibe of these sacred spaces and feels disrespectful. It's not a church but it's also not a playground for foreigners.
Explore booking some experiences on platforms like Viator or Airbnb experiences. We booked a Japanese archery lesson in Kyoto and a bike tour in Tokyo.
Happy to answer any questions but you will have a fab time planning your trip!