Itinerary

Thank you Daniel for your invaluable help so far in building up our itinerary. Sorry to bother you again due to our relative inexperience in travelling to a country where language will be a challenge for travellers like ourselves (in their 50s).
Our total stay in Japan is 14 nights.
Tokyo: 3 nights
Koa San 2 nights. It is pre arranged, where we will meet our friends for two nights.

The following places we would like to visit are:

1)Kyoto (understandably we would take some day trip to nearby places of interests)
2)Kanazawa
3)Magome to Tsumago
4)Takayama

Then return to Tokyo for one night to catch the flight back home the next day. May I add the order of the places of our intended visits is not ironclad. We would like your advice on the best way to cover these places with our JR Pass and some trip with private network of transport i.e. Trains and buses.
I thank you in advance for your contribution to make our trip enjoyable.