Cost efficiency of this itinerary

We are 3 adults who will be travelling as follows over a 10 day period (28 Oct-4 Nov): Tokyo-Takayama-Kyoto-Himeji-Naoshima-Tokyo. Would a 14 day JR Pass be cost-efficient, or would it cost less to purchase individual tickets?

Also, I understand that the bus Takayama-Shirokawago and the ferry Uno-Naoshima are NOT covered in the JR pass. Could you confirm, please, that Haneda-Tokyo and Narita-Tokyo trains are similarly NOT included please?

Thank you.