14 days in Japan - JR rail pass

Hi,

I am very confused as to where all the JR pass can be used in my Itinerary. If anyone can help me that, will be great!

My husband and I are travelling to Japan from the 29th March 2019 to 11th April 2019 to see the Cherry Blossom.

Below is my rough itinerary for 14 days.

29th (India - Tokyo)
30th (Tokyo)
31st (Tokyo - Nikko - Tokyo)
1st April (Tokyo - Hakone - Tokyo)
2nd April (Tokyo - Kyoto)
3rd April ( Kyoto - Osaka - Kyoto)
4th April (Kyoto - Nara - Kyoto)
5th April (Kyoto - Suntory Yamakazi - Kyoto)
6th April (Kyoto - Osaka - Kyoto)
7th April (Kyoto - Kanazawa)
8th April (Kanazawa - Shirakawago)
9th April (Shirakawago - Takayama)
10th April ( Takayama - Tokyo)
11th April (Tokyo - India)

From there places where all will my JR pass be used?

Also we wanted to experience a Ryokan stay and Onsen. Out of all these places which one will be the best one to experience that?

Any help would be greatly appreciated!

Thank you!
Snehi