Where can I use my pass?

Hi there!
I was hoping to get some help with the following itinerary. I have a two-week all-Japan JR pass, and I would like to understand where in my itinerary I will not be able to use the pass? What other tickets will I need to buy?

Narita Airport -- Tokyo
Tokyo (within Tokyo)
Tokyo -- Nikko - Tokyo
Tokyo -- Takayama
Takayama -- Osaka
Osaka (within Osaka)
Osaka -- Hirosihima
Osaka -- Himeji
Osaka -- Mikawa Toyota
Mikawa Toyota -- Kyoto
Kyoto -- Nara
Nara -- Koyasan
Koyasan -- Kyoto
Kyoto (within Kyoto)
Kyoto -- Tokyo

Thank you so much for the help!