Though my tastes tend more toward the rural/traditional, so if that’s less your thing, My answers might not be up your alley.

In Tokyo, the Palace, the Kaminarimon, the Edo Museum, just checking out the neighborhoods and people watching.

Day Trip from Tokyo, Nikko is really something.

Kyoto: Silver Pavilion/Philosophers’ Walk; Golden Pavilion; Heian Shrine; Nijo Castle; any garden your guidebook tells you was designed by Kobori Enshu; kokedera; Ryoan-ji; Kyomizu-dera and the surrounding neighborhood.

Give Osaka a miss unless there’s something you really want to see. I would recommend s day trip to Nara instead to see if you fit through the big Buddha’s nostril.

If you really want to see. A castle, I’d recommend Himeji, s but further west from Kobe. Or a more off the beaten path, there’s an all original castle I think called Takahashira. Still doable as a day trip in the Kansas region but would involve slower trains and far fewer people.

It’s been 20+ years since I’ve been there but any questions I may be able to answer, Fire away.