Itinerary in Japan with the rail pass...

Hi there!

Most places are indeed reachable by train and you would be able to make good use of the JR Pass!

There are some parts however that require a little extra care when planning.
Namely Jigokudani and Shirakawago. The way to Jigokudani is mostly traveled by train, you can use the Nagano Electric Railway to Yudanaka and a bus from there, the Nagano Electric Railway is a privately help railway company and requires a ¥ 1,230 fee. You can find more on how to access the monkey park HERE.

The 2nd is Shirakawago, the village has two main approaches, one is Takayama the other is Kanazawa. The fastest way from Tokyo is via Takayama while Kanazawa is better if you come from Osaka/Kyoto. The JR Pass covers the full train route to either city but you'll have to use an express bus from there to Shirakawago.

Hope this helps!
Daniel