Tokyo-Yokohama-Kyoto-Takayama-Magome-Tsumago-Koya San-Tokyo

Dear Explore Japan,
We are a couple planning to travel from Tokyo Narita to Yokohama.
After staying in Yokohama for 8 days, we plan to explore a bit of Japan in the following 8 days.

We are in doubt whether a Japan Railpass will be feasable for us, and if our itinerary is too encompassing.
We are also in doubt about the best train (or bus) connections, as well as the order of planned site visits.

We would like to travel as follows:
From Yokohama to Kyoto, staying three nights in Kyoto with a daytrip to Nara.
From Kyoto, we imagine travelling to Takayama for an overnight stay to see the Hido Village.
From Takayama, we imagine travelling to Magome and hike to Tsumago and staying overnight in Tsumago.
From Tsumago, we imagine going to Koya San for a two nights stay.
From Koya San, we imagine travelling back to Tokyo for an overnight, before flying back to Europe.

Can you advise us on our plans?
Thanks in advance!

Best regards,
CWITT