rhouses Nishiki market in Kyoto is well worth a visit. Then go eat Unagi here:
https://www.kyoto-nishiki.or.jp/en/stores/notoyo_ajisai/
They’ve been serving it since 1912.
A few temples are pretty spectacular in Kyoto: You’ve almost obliged to do the Fushimi Inari-taisha shrine, but a few others are less known and more serene IMO like Tofuki-Ji.

If you get a chance drive 1 hr out of Tokyo to Hakone and enjoy the volcanic springs and scenery there- a lot of the hotels have onsens in the rooms and you can just chill out in there.
Food-wise in Tokyo I can highly recommend:
https://www.narisawa-yoshihiro-en.com
https://azabukadowaki.com/info.html#info_en
if you want to book any high end meals in Tokyo you tend to either know people who will book for you or use this app:
https://www.pocket-concierge.jp/en
I’ve only ever gone to Hokkaido to ski so can’t really recommend any sightseeing.