Japan is awesome, you will love it!
I recommend a day trip or overnight stay in Hakone/Mt Fuji. We took a ferry around the lakes and got a lovely view of Fuji/mountains.
In Tokyo, Shinjuku station is the busiest in the world. We also spend many nights just walking around Shinjuku looking at lights, shopping and eating amazing food in little side streets.
The memorial park in Hiroshima is very sad but touching.
Night markets in Kyoto..