In Tokyo I'd add to go to the food stalls under the bridge in Ginza; treat yourself to amazing mixed drinks at Gen Yamamoto
English Craftheads is a great beer bar in Tokyo.
Go to Shibuya Crossing to see the hordes of people crossing the streets. Go to the Tsukiji fish market, even though its in a new setting its still pretty cool. Wander around the palace and visit some of the shrines. Kapabashi street is pretty cool for kitchen knives and rubber realistic food. Kyubey for sushi is about as good as it gets. The shrines in Tokyo are interesting but rebuilt for the most part. Even the harajuku area is interesting. We picked up some fancy chopsticks in Shibuya.
We took a train to Nakamora to see the Giant Gotama Buddha statue and go inside of it.
We had fun staying at an Onsen near Mt. Fuji, while we didn't climb Mt Fuji there are pirate ships on a lake, black eggs in sulfer springs, some neat hiking around the area and a cool train that zig zags up the mountain.
Kyoto is amazing. Hit the bamboo forest, the shrines like the
Fushimi Inari-taisha with thousands of Toris is amazing. These are really old and were not bombed in WW2.
We also did a train trip out of kyoto to Yamazuki for whiskey tastings.
Amazing country.