6 Week Japan Itinerary Assistance

I have been struggling through our 6 week Japan itinerary and think I am finally in a position post it and ask for any experienced opinions and assistance. I value any help. Because we have 6 weeks, we can see quite a lot of Japan. We do have quite a few 1 and 2 nighters, but generally prefer to hang our hats and have a home base for longer and venture out from there. We have not worked out where and when to activate any JR Passes yet. We would like a balance between city and country (preferably smaller, local areas & towns) and like to hike, exercise, outdoors, nature, culture, not generally in that order.
It looks like Golden Week in 2020 is from April 29 until May 5, and we would like to be settled into a "not so busy" area and for sure not travel on the start and end dates.
Some dates we are not flexible due to already having our accommodations reserved in small towns where there is not much available or we managed to get into an accommodation that we wanted. These dates are our Kumano Kodo walk, Tsumago, Koyasan and Kinosaki.
Other dates we are flexible.
So here it is...
1-4 April: Tokyo (4 nights)
5 April: travel to Magome, walk to and stay overnight in Tsumago
6-8 April: Tsumago to Kyoto, 3 nights in Kyoto, explore Kyoto
9 April: Kinosaki Onsen
10-14 April: Osaka (5 nights), explore Osaka and take day trips to Kobe, Himeji and Nara
15 April: Koyasan, temple stay at Ekoin
16 April: Kii Tanabe
17-20 April: Kumano Kodo walk
21-22 April: Somewhere between Nachisan and Kii Katsurura, want 2 nights to rest after our walk or maybe more if we are in a particularly nice place.
23-25 April: Hiroshima and Miyajima (3 nights between the two places)
26-27 April: Onomichi, cycle the Shimanami Kaido
28 April - 1 May: Kanazawa or surrounding area (4 nights), drive the Noto Peninsula, and either from Kanasawa or Takayama we want to visit Shirakawa-go or Ainokura
2 -5 May: Takayama (4 nights)
6-7 May: Nikko (2 nights)
8-10 May: Tokyo (3 nights)
We are fairly happy with our itinerary up to the finish of our Kumano Kodo walk (20 April), but are definitely open to suggestions. From 20 April onwards, we are uncertain. We have outlined where we would like travel too, but are unsure of how many days and any other sites that we are missing. Happy for any input.