Kyoto-Tokyo - suggestions?

In October I will visit Kyoto for a business trip - my first time in Japan. There will be some time for seeing Kyoto with my hosts, and I am able to follow this with one week of independent travel before flying home.

I am not a great fan of big cities and night life but would like to travel on the shinkansen and see Tokyo for maybe 1 full day (2 nights). I would also like to stay in a ryokan somewhere. I thought that Takayama and Shirakama might be a good place to go in between Kyoto and Tokyo. If anyone has comments on this they are welcome!

How would you recommend to split the time between Tokyo and Takayama/Shirakama/elsewhere? Is it easy to do day trips from Tokyo to places that are less crowded? Often this is easier (no luggage) than staying in a new place every night or two.

I am interested in seeing a few good examples of Japanese culture and landscape, and enjoying Japanese food. I enjoy photography and can happily spend time photographing parks, temples, markets, people etc. I like activities such as walking/hiking, cycling, and boat trips. I don't enjoy theme parks and zoos so much.

Can anyone suggest a place or two that I might like to visit?

Also, from what I can see I do not think a Japan rail pass will be good value for me, and I should get individual tickets - do you agree?

Thank you in advance for any advice!

A suggestion:

Kyoto - Kanazawa (1-2 night) - Shirakawago (1 night) - Takayama (1-2 nights) - Matsumoto (0-1 night) - Tokyo

Kanazawa:
http://www.japan-guide.com/e/e2167.html

Matsumoto:
http://www.japan-guide.com/e/e6050.html

Thank you!

I have found that I will be travelling at the exact time of the Takayama October festival - my chances of accommodation as a single traveller there are not so good now!

So I think I will take your suggestion of Kanazawa for 2 nights, then go to Matsumoto via the Tateyama Alpine route, and stay 1 or 2 nights before heading to Tokyo.