So sorry I have only just gotten to this @tea.
My number one recommendation is to purchase your rail pass before you go. It’s cheaper hear and also one less thing you have to worry about.
I love everywhere I went. Tokyo, Yamanouchi, Osaka, Kyoto, Nara, Hiroshima. I highly recommend the free Mazda Tour in Hiroshima (even if you’re not into cars). It’s pretty cool and you get to see how the factory floor works, it’s pretty cool. Plus Hiroshima has amazing history and the shrines set up from the atomic bombing are very sobering. It is a must see in the political climate we live in. I am a vegetarian and found it hard to eat at times, but there is a phenomenal vegan ramen restaurant in Tokyo station. I mean phenomenal!!! It was the tastiest thing I have ever eaten. My partner is not a vegetarian but we kept going back because they were just so good. It’s Called T’s Tan Tan. Another great thing to do is go to Piss Alley (don’t let the name fool you) in Shinjuku is awesome too. Filled with little yakatori restaurants that seat max 6-7 people and way over pour their sake (perfect!). Yamanouchi is a pretty cool place. It’s close to where the snow monkey park is. The monkey’s are those ones that people have probably seen in nature shows where they bath in the natural springs throughout winter. Def a must do if you are looking at going up that way.
I’m sure you’ll find plenty of things to do. We stumble across a lot of things and I think that’s a nice way to do it. Just walking and finding things with only a few main things planned for the days.
Hope this helps 🙂