7 day HND-Kyoto-Kanazawa-Shirakawa-Takayama-Toyama-Tateyama Kurobe Alp route-Hakone-Tokyo

Hi,
I know, it's very tight with my itinerary ;-))

I already buy JR PASS, my question is :
where area (in my itinerary), not covered by JR Pass ?
a. HND-Kyoto = Keikyu line to Shinagawa and Hikari shinkansen to Kyoto
b. Walking around Kyoto like a Fushimi Inari, Kiyomizudera, Arashiyama, Gion district (my hotel in Kyoto station)
c. Kyoto-Kanazawa = LTD.Exp.Thunderbird
d. Kanazawa- Shirakawa = Nohi bus
e. Shirakawa - Takayama = ??
f. Takayama - Toyama = ??
g. Toyama - Shinano Omachi =Kurobe Alp.option
h. Shinano Omachi - Odawara = ???
i. Odawara - Gora (hakone) =???