Itinerary help, 7 days around Chubu/Kansai

I am traveling to Japan for 17 days this November! Would love help figuring out the middle part of my trip (loop around

Nov 9: Arrive in Tokyo and stay 3 nights
Nov 12: Mount Koya
Nov 13–17: Kyoto with day trips to Naoshimi and Himeji
Nov 18: Kiso Valley
Nov 19–22: Tokyo with day trip to Nikko
Nov 23: Hakone
Nov 24–26: Tokyo

Questions:
1) I'm torn about adding Shirakawa-go. It looks so beautiful. Is it worth adding? Where would you add it in the trip?

2) Do you think Kiso Valley will be after-peak for autumn leaves by Nov 18? Should I push that earlier (swap with Mount Koya)?

3) Will Nov 23 in Hakone be super busy and crazy? Noticed it's also a holiday in Japan. We're Americans so we're "celebrating Thanksgiving".

4) Generally, do you think this is a balanced trip? Missing anything or too fast paced? I'm a bit worried about burn-out. I'm also worried about only hitting spots that will be super-touristy. I wonder if I should pick some places that are more off the regular path.

(1) Only you can answer your question. If you want to add Shirakawago, I suggest you drop few days in Tokyo, and go to Kiso and Shirakawago before Kyoto (and move Mt Koya after Kyoto).
(2) Autumn leaves are hard to predict, especially if you are trying to hit it with just a one day window. 2016 season came late because of a longer summer.
(3) Hakone is always busy, and more so during holidays. Make your reservation early.
(4) It is not well sequenced in my opinion. [a] Mt Koya from Tokyo takes too long, you need to add one more night or go after Kyoto; [b] Naoshima is too far from Kyoto for a day trip; [c] you have 3 segments in Tokyo - that is too inefficient.

Thanks for the help!

OK, so my updates:

- Kiso first, between Tokyo and Kyoto.
- Koyasan second, after Kyoto. Then go from Koyasan to Tokyo.

I'm going to ditch Naoshima unless I get a strong urge while I'm there and maybe I'll stay a night there.

Unfortunately I am meeting friends in Tokyo then going to Hakone ... I don't see many options to combine the Tokyo segments.

I think Koya-san to Tokyo in 1 days is too long as well. When my wife & 1 did Tokyo to Koya-san we went Tokyo to Kyoto, spent 2 nights in Kyoto, then overnight in Koya-san, then back for 2 more nights in Kyoto, then back to Tokyo. Even then it felt rushed (and I've been to Kyoto many times so we didn't do all the most crowded tourist sights).

Hmm okay thank you.
It seems like it's about 4 1/2 hours from Koyasan to Tokyo.
I know that's a long time but I was thinking that my schedule would be:

- Arrive previous day in Koyasan in the afternoon, from Kyoto.
- Stay the night.
- Spend the morning and afternono in Mt. Koya.
- Around 4pm, head to Tokyo.
- Arrive in Tokyo in evening around 8-10pm.

Do you think that doesn't work? Do trains not typically run that late? I'm not sure quite how to tell - I used Google Maps and put in a 4pm departure for a 4 1/2 hr travel time.

If you plan to just sleep upon arrival in Tokyo from Koyasan, then your plan works fine. The 4.5 hr estimate may be the time on trains, the total elapse time (including transfer time) will likely be a little over 5 hours. But trains run until late in Tokyo, so it is not as bad as going to Koyasan.