Ryokan and itinerary advice for November trip

I'm going to be in Japan from November 18 to December 1st and my partner and I have decided on a set of regions we will stay during the trip but we are having some trouble picking the order of things.

1. We want to spend some time in the region near Kyoto checking out Kyoto, neighbouring areas, Nara, and hang around the Mie prefecture (we have a friend there).

2. We will spend some time doing a sort of road trip that starts Shirakawa-go and ends in Nikko (or vice versa). During this section of the trip I think I want to stay at a Ryokan (with full meal service) near Takayama or the Okuhida region. In general I am more interested in more rural and mountainous onsen/ryokan than a bigger ryokan so this region seems good.

3. We will spend some time in Tokyo and the region surrounding Tokyio.

As of now, the total number of days I have allocated is as follows: 3 nights for the Tokyo region, 5 for Kyoto section, and 4 for the Nikko/Takayama road trip section. Is that a good allocation? Originally I had thought it best to land and immediately start the Kyoto section of the trip for the fall colours but now I wonder if I should start the trip in the Nikko - Takayama section to increase my odds of getting fall colours during my ryokan stay. Thoughts?

Lastly, do you guys have suggestions for Ryokan in the Okuhida/Takayama area? I'm having trouble searching online and specifying full meal service. Something smaller and mountainous is preferred but not required. I know there are 5 onsen towns in Okuhida and I'm not sure which to pick. Thanks for the help!

Hi.
I think I'd start with the Kyoto section first. Full colour is in the second half of November, the winds pick up and things brown off in late November, in my experience and its all looking pretty red and brown by the beginning of December. I'd have thought that if you start at Takayama/Nikko first you run the risk of getting there past peak and getting to Kyoto past peak.
For ryokans I have stayed at Tanabe Ryokan in Takayama a few times, it is very nice. But if you havent stayed in a ryokan before I'd suggest Tsuruya Ryokan at Karuizawa which is in a nice part of the town on the way back to Tokyo. Or one of the places in Bessho Onsen. Have a look at the sites "japan guest houses" or "secret onsen" for something you might like.
I dont know whether I would include Nikko in your middle section. Ultimately if I was coming from Kyoto, I'd look at stopping at Hikone for the castle, then Takayama, then bus to Matsumoto, then train to Karuizawa or Bessho Onsen before getting back to Tokyo. Then I'd do Nikko as a day trip or overnight stay (Hotel Kanaya is great).