Wow, you plan to be very busy for 2 weeks.
The bus from Takayama to Shirakawa-go will take about 90 minutes and is run by Nohi Bus not JR so you will have to pay for that part of your trip. See
Hida Takayama Nohi Bus
Of course it could not hurt to ask when you buy your ticket if you can use the JR Pass. The worst they can say is "no".