Tokyo - Hakone - Kanazawa - Shirakawago - Takayama - Jigokudani - Tokyo

Hi!
I would like to do an itinerary check and if the JR pass would also cover the freepass / day pass
like the Hakone Freepass (that includes the Ropeway), Kanazawa Loop / Excursion Bus / Light Up Bus.

Here is what's we have in mind

Saturday - Narita to Tokyo
Sunday - Tokyo to Hakone
Monday - Hakone to Kanazawa
Tuesday - Kanazawa to Shirakawago and Takayama
Wednesday - Takayama to Nagano / nearest station to Jigokudani
Thursday - back to Tokyo
Will then be in tokyo till the next tuesday.

I've did a calculation on the total travel fare between the said locations and buying a JR pass is cheaper, however I'm also concerned if it can be used for bus / shuttle within the smaller town itself.

Thanks :)