Itinerary Help

Hello!

Me and my partner will be travelling to Japan end of October.

At the moment we have planned Kyoto for 4 days at the start and Tokyo for 5 days at the end. We have 5 days in the middle to get from Kyoto to Tokyo.

We would like to do something a little more nature, less city. We will have JR pass. However, happy to train from Kyoto to point A and hire a car, then return it to point B and train to Tokyo if thats easier/better.
Or fly.
Or a tour.
Any and all the options! :)

What can you recommend please??

I've done a lot of research on this site and many others and I think I am a little overwhelmed and just stuck.....

A simple option is Kyoto-Takayama-Kanazawa-Nagano-Tokyo.
Or you could do Kyoto-Kanazawa-Nagano-Tokyo.
Option #3 (did this a few years back), Kyoto-Matsumoto-Nagano-Tokyo, however, you could also use the route from Matsumoto to Kofu and Kawaguchiko, and then to Tokyo.

Can you explain your need for a rail pass? I fail to see the need it you start in Kyoto and finish in Tokyo.

Nara. Add Nara to your Kyoto itinerary, if it isn't already. It can be a day trip from Kyoto. One day.
https://www.japan-guide.com/e/e2165.html

Ise Shima. If you use the JR Pass, transfer at Nagoya. You still need to pay a little extra, as one segment of the trip runs on non-JR track. One day. https://www.japan-guide.com/e/e4310.html

Hakone. Enjoy onsen and other sights. Use the JR Pass to Odawara, then transfer to a non-JR train. Two days. https://www.japan-guide.com/e/e5200.html