Unless you're arriving early in the morning from Australia or New Zealand, your first day in Tokyo is too ambitious. Flights from North America to NRT generally arrive after 3:00PM, and even if you make it through customs and immigration in record time, NRT is 60km/40 miles out of the city, and you will be jetlagged.

If you're flying into HND, you'll probably get there very early in the morning, still jet lagged.

Are you going to fly to Osaka or take the train?

There really aren't any overnight trains between Tokyo and the Kyoto/Osaka area. They're only about three hours apart by Shinkansen. Just take the Shinkansen straight to Kyoto. Much less hassle, downtown to downtown.

I guess you haven't looked at a map to see how far Himeji is from Kyoto.

Nagasaki-Hiroshima-Osaka in one day? No, no, no. Not even by plane.

If you're flying out of KIX, be aware that it is not in Osaka but 40km south. There are convenient trains from both Osaka and Kyoto.