Having lived in Japan for two years, what I'd add to this is to spend a lot of time walking, if physically able. For example, in my opinion the best way to explore Tokyo is to simply leave your hotel in the morning, wander around all day, and stop anywhere and everywhere that looks interesting. The excellent mass transit system means that it won't be a problem to get back. In more rural parts of Japan, there are sign…
Tokyo is absurdly gigantic, I would not suggest randomly walking it. Also the subway system can be challenging, and the staff don't speak English, so if you get stuck they likely won't be able to help. Another random thing about the train system: there are women-only cars. I didn't realize this until I had already boarded and (as a man) I was absolutely mortified.
The Tokyo subway system is massive but not challenging. Everything is surprisingly systematic and consistent (unlike NYC's MTA which is legacy with express/non-express trains and cars with doors that don't open in certain stations) and with Google Maps, I had no problems getting anywhere with no backtracking. Announcements and notices are bilingual Japanese/English. Staff don't speak English but I've never had to speak to anyone -- the system is just so intuitive. In most subway systems around the world, you really almost never have to speak to anyone. Don't have Google Maps? Look at the subway map. It's big, but all you have to do is locate your destination and know where you are -- easy. The Japanese are great at creating intuitive visuals.
The female-only cars are common around the world (Rio has them too), not sure why it is a cause for mortification. There's a reason why they exist, and that reason exists in North America too.
Tokyo is big but extremely navigable for a foreigner.