3 Week Itinerary for November

Planning to go back in November for 3 weeks. We've already been to Tokyo, Osaka and Kyoto (and all the popular day trips from those places), so this year we're looking to mainly do some other things. We've put in 2 days of Kyoto as we didn't cover everything last year and it would be a nice stop on the way back to the Nagano/Kanto area.
Please let me know your thoughts on the below schedule. We are planning on using a 21 day JR Pass.
Date Place of Stay Activity
4-nov Flight
5-nov Tokyo Arrival 9AM
6-nov Tokyo Daytrip Kawaguchico (Mt Fuji)
7-nov Tokyo Daytrip Nikko (Ryuzu/Yudaki/Shoyoen)
8-nov Tokyo General/Leave for Hiroshima in evening
9-nov Hiroshima Peace Park /Atomic Bomb Dome/Shukkeien/ Downtown
10-nov Hiroshima Daytrip Miyajima
11-nov Hiroshima Daytrip Ōkunoshima (Bunny Island) + Onomichi (Kosanji/Templewalk)
12-nov Hiroshima General/Leave for Nagasaki in evening
13-nov Nagasaki Hashima island
14-nov Nagasaki General/Leave for Fukuoka in evening
15-nov Fukuoka Nanzoin Temple / Canal City Hakata
16-nov Fukuoka General/Leave for Kyoto in evening
17-nov Kyoto General
18-nov Kyoto General
19-nov Kanazawa
20-nov Takayama Daytrip Shirakawa-go
21-nov Takayama General/ Leave for Tokyo in evening
22-nov Tokyo
23-nov Tokyo
24-nov Tokyo
25-nov Flight Departure 11AM

We were thinking about Kumamoto, but read that the main attractions are closed off due to the earthquake in 2016, as well as a daytrip to Volcano Aso. I'm not sure if the travel time will be worth it, considering the fact that the main stuff in Kumamoto is closed and the Volcano trip also takes 5h (go+return).

Please let me know what you think. We can always swap a day in Tokyo out for something else. Any tips/whatever are also welcome.

Kawaguchiko and Nikko are far from Tokyo as day-trip destinations. Both are more convenient with non-JR operators. Mt Fuji is usually better in early morning. Yudaki and Ryuzu are far from Toshogu, more than one hour to get to. Onomichi is full of temples, but Kosanji is on Ikuchijima island. So, Okunoshima + Kosanji + Onomichi would be a long day trip. A tour to Gukanjima (Hashima island) would fill up a whole morning. Takayama-Shirakawago-Kanazawa is better with Nohi bus rather than JR.

Kumamoto & Aso: http://kumanago.jp/whatsnew/?mode=detail&id=421
Aso: http://www.asocity-kanko.jp/en/top/

I think of

A flight to Tokyo
Kawaguchiko by Fujikyu Bus and Nikko by Tobu trains
A flight to Nagasaki http://www.japan-guide.com/e/e2364.html
A 14 day Japan Rail Pass?
A flight out from Nagoya

but, here is an another one:

5 Nov TYO-Nagasaki(2N)
6 Nov Gunkanjima(tour)
7 Nov Nagasaki-Hakata(2N)
8 Nov Nanzoin Temple + Canal City Hakata
9 Nov Hakata-Hiroshima(4N)
10 Nov Miyajima
11 Nov Peace Park / Atomic Bomb Dome / Shukkeien / Downtown
12 Nov Okunoshima + Kosanji + Onomichi
13 Nov Hiroshima-Kyoto(3N)
14 Nov Kyoto
15 Nov Kyoto
16 Nov Kyoto-Kanazawa(2N)
17 Nov Kanazawa
18 Nov Kanazawa-Takayama(2N)
19 Nov Shirakawago
20 Nov Takayama-Kawaguchiko(2N)
21 Nov Mt Fuji
22 Nov Kawaguchiko-Nikko(2N)
23 Nov Yudaki + Ryuzu + Shoyoen
24 Nov Nikko-Tokyo(1N)
25 Nov TYO

An example for Onomichi day:
Hiroshima 641-753 Tadanoumi https://world.jorudan.co.jp/mln/en/?p=0&from=Hiroshima&to=Tadano-Umi&d...
Tadanoumi 830-845 Okunoshima(2h) https://www.qkamura.or.jp/ohkuno/access/images/time.pdf
Okunoshima 1050-1105 Tadanoumi
Tadanoumi 1120-1136 Sunami https://world.jorudan.co.jp/mln/en/?p=0&xpd=1&from=Tadanoumi&to=Sunami...
Sunami 1150-1218 Sawa http://habushosen.com/timetable/timetable05
Sawa/Kosanji(2h)/Setoda
Setoda 1510-1549 Onomichi(2h) http://www.s-cruise.jp/map/#map03
Onomichi 1753-1855 Hiroshima https://world.jorudan.co.jp/mln/en/?p=0&from=Onomichi&to=Hiroshima&dat...

Setouchi transportations. Kosanji is near Setoda/Sawa between Okunoshima and Onomichi. You need to stop at three sites in a day.
Okunoshima/大久野島
- Sunami/須波, Mihara/三原, Sawa/沢, Setoda/瀬戸田
- Onomichi/尾道
map: http://habushosen.com/boarding

JR Tadanoumi/忠海 - Okunoshima
ship: https://www.qkamura.or.jp/ohkuno/access/images/time.pdf

Okunoshima - JR Sunami - JR Mihara (Only on weekends)
ship: http://habushosen.com/timetable/timetable08

JR Sunami - Sawa
ship: http://habushosen.com/timetable/timetable05

JR Mihara - Setoda
ship: http://habushosen.com/timetable/timetable06
ship: http://marutokisen.sakura.ne.jp/main-page/timetable2.htm

Setoda - JR Onomichi
ship: http://www.s-cruise.jp/map/#map03
bus: http://onomichibus.jp/route-bus/timetable2015_10/setoda-line.pdf