Please help with our itinerary...

Hello Japan!

My wife is just about complete with the final draft of our itinerary. We would like a second opinion on what she has decided on. She’s the boss. :)
We will be arriving in Narita airport on 2/28 in the late afternoon and staying by the Tokyo Station for 2 nights.
3/1 - Day 1 in Tokyo.
3/2 - Day 2 activate our 14-day JR Pass and travel late in the afternoon from Tokyo to Takayama.
3/3 - Day 3 in Takayama. Stay overnight in Takayama.
3/4 - Day 4 we’ll travel early from Takayama to Shirakawago. Then, later in the evening travel from Shirakawago to Kanazawa. Stay 3 nights in Kanazawa.
3/5 - Day 5 in Kanazawa.
3/6 - Day 6 in Kanazawa.
3/7 - Day 7 we’ll travel early from Kanazawa to Kyoto. Stay 5 nights in Kyoto but here’s where it get’s tricky:
3/8 - Day 8 we’ll travel early from Kyoto to Hiroshima and Miyajima Island. Later in the evening, travel back to Kyoto. 3/9 - Day 9 in Kyoto. 3/10 - Day 10 in Kyoto. 3/11 - Day 11 we’ll travel early from Kyoto to Mt Koya. Later in the evening, travel back to Kyoto. 3/12 - Day 12 we’ll travel early from Kyoto to Nara. In the very late evening, travel from Nara to Hakone (Do they have a very late train or is it better to spend a night in Nara?). I hear they have a festival going on in Nara.
3/13 - Day 13 we’ll either travel early from Nara to Hakone, or, we’re already in Hakone and will spend a night in Hakone.
3/14 - Day 14 we’ll travel early from Hakone back to Tokyo. Our flight leaves early in the evening.

There are some places I'm interested in seeing, but unsure if they are easily accessible with the JR Pass:
Kyoto: Fushimi Inari, bamboo forest, Nijo Castle
Hiroshima: Miyajima Island
Nara: Deer park, Todai-ji

We would greatly appreciate any recommendations to make our itinerary easier although the wife spent a lot of time planning.

Thank you so much for your help. We can’t wait to see your beautiful country!

Sincerely,
Olena and Charles