Itinerary Japan

Hi
We are looking at fooling itinernary in September and don't want to spend too much time travelling. We would prefer to be based longer in 1 spot where possible
Tokyo 3 nights
Kanazawa 2 -3 nights
Takayama 2 nights
Kamikichi 1-2 nights ???
Matsumoto 2 nights
Tsumago 1-2 night ??
Then would like to go to Mount Fuji & Hakone, I'm not sure the bet way to get to Mount Fuji from Tsumago or whether it would be better to go to Nagoya and then to Hakone and skip Mount Fuji . I would appreciate any advice

Fuji is an easy day trip from Tokyo. Return to Tokyo at the end of your trip and visit the Fuji area then.

great trip. only one suggestion:
after takayama instead of two days in Kamikochi, i would take one day in Okuhida Onsen (e.g. 隠庵 ひだ路 or 槍見の湯 槍見館 or Hirayu) and the other day in Kamikochi (so one day for each place).

In Okuhida you could do the "Village of Folklore" (昔ばなしの里) or the "Shinhotaka Ropeway" for example

both places are not very far apart, so moving will be not much of trouble, there are even buses (if needed), but scenery (and also onsen) is different