My husband and I will be travelling to Japan January 28 through to February 14th. We are hopeful to do most of our travel via rail with a 14 day Japan Rail Pass. We are starting off in Tokyo (4 nts) on to Yudanaka (2 nts). From that point we were planning on heading to Takayama (2 nts) and then on to Kyoto for (5 nts). In addition to this, we wanted to go back and spend time in Hakone and/or either Mt. Fuji Five Lakes region. We already have some hotel reservations made, but am not quite sure of which direction or order of travel we should take. I have done a lot of research on the JP Rail Pass and know most of this is quite doable. We will be flying in and out of Haneda. Any advice with the order of itinerary would be most helpful and appreciated.
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If you are going to the Mt Fuji area, it would probably make the most sense to do so at the start of your trip, or returning back from Kyoto. If the former, you can use an Odakyu pass from Tokyo which would give you more time to travel to the other places you are going to.
http://www.odakyu.jp/english/deels/
If you are going to visit Kyoto, then you should not miss Nara either - skipping the Todaiji Great Buddha would be a tragedy. You could also take a day trip to Himeji if you like, and see Osaka in the evening after a day in Kyoto.
You can find regular rail fares, routes and schedules on Hyperdia.
http://www.hyperdia.com
Under "More Options", be sure to uncheck the Nozomi box if on a JR Pass since you can't ride that train using the pass.
You can see previews of some of the best places to see in Japan on:
https://www.youtube.com/user/thejapanfaq/videos
There are also loads of other tips on
http://www.thejapanfaq.com/the-best-japan-travel-tips/
Best regards.