Asking help with 15 days itinerary

Hello!
I'm going to Japan in November (arrive at Tokyo-Narita - 19th November morning - and leave at 04th December ,in the morning). Because this is my first time in Japan I would like to see most of the must see cities, scenery, nature. Therefore I would like to ask for some advice from people that already have been there and can give any feedback if I need to reduce or to increase days in each city etc.

We would like to plan an itinerary that lets us experience Japan using 7/14 day Rail Pass.

Our preliminary plan looks like this:

Tokyo (Narita)-straight to Kyoto (5 full days in Kyoto, including trips to Nara and Yamazaki distillery)- Koyosan (1 night)- Kanazawa - Kanazawa via Sirakawago- Takayama – Matsumoto (not sure if to include)- Hakone or Kawaguchico (not sure if to include and if which one) –Tokyo (4 full days in Kyoto, incl. 1 day trip either to Kamakura or Yokohama).

I would be grateful for some feedback as I need some clarification:

(A) re travel to Takayama-Shirakawago- Kanazawa. How long I should stay at each places? If Takayama 2 nights, Kanazawa 1 night or 2) Takayama 1 night, Kanazawa 2 night. Or if my plan is too packed , to drop f.e. Takayama or Kanazawa and stay in one place for a night? Both sounds interesting, but I am not sure if I like to have a new place to stay every night.

(B) Also I am not sure which is better option:
Kyoto-Koyosan-kanazawa- shirakawago- takayama- Matsumoto (?)-Hakone (?)- Tokyo or
Kyoto- Koyosan-takayama- shirakawago- kanazawa- Matsumoto (?)-Hakone (?)- Tokyo

(C) Is Koyasan OK to reach from Kyoto and them to go to Kanazawa or Takayama? Acc. to my plan it would be during the weekend, so maybe not su great idea?

(D)I was thinking of 1 in a Ryokan in Hakone. But maybe I can book it in Takayama and then drop the Hakone to have more time in Tokyo?

(E)Tokyo/Kyoto: Is better to do in one timeframe at the beginning or end? As I�fve read November is the high season due to fall foliage, so just thinking how to avoid (if possible) crowds by doing Kyoto at the beginning or at the end of the trip?

(F)Am I trying to fit in too many places? Do I need more time in Tokyo/ Kyoto? What to add or remove?

Sorry about all the questions and thank you for any feedback and help in advance.

Will you fly in/out Narita? Then JR pass 14 days will be better. As you mentioned the end of November is very high season in Kyoto, even in wider area in Kansai including Osaka. Tokyo is not that crowded, as judged from the hotel rate. If you want to stay in a hotel room with private bath, Kyoto will be very expensive for your itinerary. December is somewhat cheaper for some hotels though. We can not predict the best days for autumn foliage in Kyoto now, but in recent years the dates tend to be later, sometimes in the early December though the room rate is higher in late November. Anyway, have you checked the hotel in Kyoto? You might better check the hotel in somewhat remote places such as Nagoya which is 35 min away from Kyoto (by Shinkansen).