2 week trip advice

Hello,

My parter and I will be in Japan for the first time for 2 weeks in November. I am struggling to work out if it will be worth purchasing a JR pass or just paying for tickets while we are there

We will be travelling between the following places:

Narita airport > Saitama, Tokyo
Tokyo> Hakone
Hakone > Kyoto ( we will also do day trips in and around Kyoto, inculding to lake Biwa)
Kyoto > Hashimoto (Koyasan)
Hashimoto > Tokyo (via Osaka perhaps?)
Tokyo > Narita airport

I have been trying to use Hyperdia to work out if my train tickets will cost more than the JR pass but I am getting very confused! Any help would be greatly appreciated, thank you :)