Tokyo-Hakone-Kyoto-Nikko-Tokyo

Hi, this is my first time to Japan for a 12 day visit. My tentative itinerary is:

Tokyo - 4 days
Hakone - 3 days
Kyoto - 3 days
Nikko - 2 days
Tokyo

Please advise the following:
a) Am thinking of buying the 7 day Japan Rail Pass for travel from Tokyo-Hakone-Kyoto-Nikko. Please confirm that it makes sense to do so.

b) Please advise on how I can get from Kyoto to Nikko via Japan Rail Pass. How long will it take?

c) Nov 23 is a national holiday in Japan. Will it be difficult to book accommodation across Japan? Do we need to pay a premium for booking accommodation during the national holiday?

d) Do you have recommendations for Minshuku in Kyoto?

Thanks in advance.

a: Yes, it makes sense. The cost of return Shinkansen between Tokyo and Kyoto alone makes the JR Pass worthwhile. Adding extra stops just makes it even more value for money!

b: Kyoto to Nikko involves bouncing through Tokyo. Get the Shinkansen from Kyoto and hop off at Shinjuku, then swap to the Shinjuku-Nikko Limited Express. Probably about 5 hours' travel in total, as you can't get the fastest Shinkansen from Kyoto to Tokyo with your JR Pass.

c: The Japanese tend not to charge you extra for hotels just because it's a national holiday - they don't operate quite like Western ones in that regard. However, you can expect rooms to be limited, so book as early as possible to avoid disappointment.

d: I can't help with this one, as I usually use hotels. However, you can try http://www.japaneseguesthouses.com/db/kyoto/index.htm who will also enable booking in English for you.

Naturally I only find the other website I wanted to list after I've posted :)

For Minshuku, try http://www.minshuku.jp/english/kyoto.html

Nov 23 is a national holiday in Japan. Will it be difficult to book accommodation across Japan?

No, not across Japan. But in certain cities it will be difficult, especially in Kyoto.

Do we need to pay a premium for booking accommodation during the national holiday?

Usually no. Some ryokan charge more on weekends and holidays than regular weekdays.