Hi there,
The JR Pass will be valid for all the parts of your trip with some exceptions:
Shirakawago
Shirakawago can only be accessed by car or bus, so you should check out the [Nohi bus company] which has buses that leave from both Kanazawa and Takayama. Shirakawago is roughtly equidistant from both cities, and you can take the bus from Kanazawa to Shirakawago to Takayama for ¥4200.
Kamikochi
For Kamikochi from Takayama you'll need to again take the Nohi bus. First to [Hirayu onsen], and [from Hirayu onsen to Kamikochi]. [Here are the directions from Kamikochi to Matsumoto] which are also non-JR operated.
Fuji Five Lakes (Kawaguchiko)
For Kawaguchiko, the JR Pass will get you as far as Otsuki, where you will have to change to the non-JR operated Fujikyuko line to Kawaguchiko (approx ¥1100 each way).
Koyasan
For Koyasan, the JR Pass will get you to Osaka station, where you should change to non-JR Nankai lines to take you up to Koyasan. Here's a sample itinerary from Tokyo.
Planning your trip
You can look up precise train timetables and costs at the Hyperdia travel planning website and learn how to use Hyperdia for JR Pass holders through our video blog.
Of course, you can check back here anytime if you get stuck!
Hope this helps!
