Kyoto/Koyasan/Takayama/Ogimachi/Inami

Hi, we have booked our flights to Tokyo from 25Dec till 4Jan. As we have visited Tokyo before, we are planning to visit Kyoto and trying to fit in places in Gifu/Toyama in between.

I recently found out most places will be closed during the New Year period so am trying to plan the trip around it.

My husband and I are both architects. We like to visit a couple of buildings near Toyama but can't find opening times during the New Year period (see below). Any ideas?

So far the itinerary is as follows:
25Dec Arrive Tokyo am
26Dec Inami woodcarving museum, Mountain Pavilion in Bambajima (Toyama)
http://www.archidose.org/Oct04/100404.html
Not sure if they are open at this time of the year.
27Dec Ogimachi
28Dec Takayama
29Dec Kyoto
30Dec Kyoto
31Dec Koyasan
01Jan Osaka (visit Kansai airport)
02Jan Tokyo
03Jan Tokyo
04Jan am flight home

Questions:
1. Should we get the 7 days JR pass and supplement some trips with single tickets?
2. We will rely on train and bus for all the journeys. Will any routes be non feasible in snowy winter?
3. We have booked 31Dec at Muryoko-in in Koyasan to welcome the New Year. Is this a good move?
4. I left the first days of Jan in Osaka and Tokyo as I thought more places will be open, is my assumption right?
5. If Toyama and Takayama are too difficult to visit during late Dec and due to New Year closure, what alternative itinerary will you suggest?

Many thanks for any advice. This is my first stab at the itinerary, will be pleased for any feedbacks.

I recommend you to visit Japan Open-Air Folk House Museum near Tokyo.

Japan Open-Air Folk House Museum;
http://www.city.kawasaki.jp/88/88minka/home/minka_e.htm

About the closing days for the wood carving museum, the official website mentions "New Year period". Usually that does not start before the 29th of December:
http://www.inamichoukoku.com/kaikan/index.html

But to confirm, I recommend to make a phone call:
+81-763-82-5158

The museum is also closed on the 2nd and 4th Wednesday of each month.

Should we get the 7 days JR pass and supplement some trips with single tickets?

Yes. But I am afraid that you might be under-estimating the time it takes to get from place to place, especially in the Toyama/Ogimachi region. It might be better to allocate an additional day to that part of your itinerary.

Note also that the fastest train from Tokyo to Toyama (via Echigo-Yuzawa) is not fully covered by the Japan Rail Pass. Therefore, I recommend a different order of destinations:

Tokyo - Takayama - Ogimachi - Inami - Kyoto - Koyasan - Osaka - Tokyo

We will rely on train and bus for all the journeys. Will any routes be non feasible in snowy winter?

You should be able to reach all the destinations. Only during or immediately after a snow storm might some bus services in the Ogimachi out of service temporarily.

3. We have booked 31Dec at Muryoko-in in Koyasan to welcome the New Year. Is this a good move?

I can only imagine this to be a wonderful experience. It is one of the holiest places in Japan on the holiest day of the year.

I left the first days of Jan in Osaka and Tokyo as I thought more places will be open, is my assumption right?

January 1 is the day with the most closures. However, in recent years, more and more shopping centers are also open on January 1.

If Toyama and Takayama are too difficult to visit during late Dec and due to New Year closure, what alternative itinerary will you suggest?

New Year closures affect all regions of Japan. I think ot is no reason to change plans.

Many thanks for the suggestions and tips. Will get back to my planning.