When will you travel?
Will you leave Japan from Kansai Airport [KIX], or get back to Kanto and fly out from Haneda [HND] or Narita [NRT]?
Do you aim to climb Mount Fuji, or just hope to have a close view of the hugest mountain in Japan?
You can make a one day round trip from Tokyo to around Lake Kawaguchiko among the Fuji Five Lakes; you might hope to stay overnight and go around the five lakes.
Or, you can make a side trip to Hakone from Odawara on the route (along the Pacific Coast) from Tokyo for Nagoya and Kyoto.
Instead of heading straight to Kyoto, you can go northbound from Nagoya to Takayama, Shirakawa-go and Kanazawa in this order then southbound from Kanazawa to Kyoto.
How long to spend looking around Takayama, Shirakawago and Kanazawa please? That depends on your pace, preferences and destinations.
In Shirakawa-go, a fast traveler could go around Ogimachi district within several hours, but there are still farmhouses where a lodgement service is offered to tourists; please pay attention to the closed days of sightseeing facilities.
In Kanazawa, when you plan to go around two or more areas, I recommended you stay overnight.
Some related Japan Guide articles
- Fuji Five Lakes travel: Lake Kawaguchiko
https://www.japan-guide.com/e/e6906.html- Hakone Travel: Hakone Round Course
https://www.japan-guide.com/e/e5210.html- Hakone Free Pass (Hakone Freepass)
https://www.japan-guide.com/e/e2358_008.html- How to travel between Takayama and Nagoya
https://www.japan-guide.com/e/e5908.html?aFROM=2155_5900- Shirakawa-go & Gokayama Travel:
Overnight at a gassho-zukuri house
https://www.japan-guide.com/e/e5952.html- Bus Timetable: Takayama - Shirakawago - Kanazawa/Toyama
https://www.japan-guide.com/bus/shirakawago.html- How to travel between Kanazawa and Kyoto
https://www.japan-guide.com/e/e4208.html?aFROM=2158_2167- Takayama-Hokuriku Area Tourist Pass
https://www.japan-guide.com/e/e2361_takayama_hokuriku.html