Best transport passes for my trip

Hi!

I am looking for the most cost effective combination of transport passes.
I believe I will require a JR Pass (although I am not sure if I should get the 'national' one or region specific - i.e. 'kansai' for Kyoto and 'East south Hokkadio' for the end of my trip)

My trip is as follows; any advice would be great! Thanks

Arr. Date Dep. Date Nights Destination: Day Trips
29-Nov-19 02-Dec-19 3 Nagasaki
02-Dec-19 04-Dec-19 2 Fukuoka: Yufuin(?)
04-Dec-19 07-Dec-19 3 Hiroshima: Miyajima Island, Matsuyama(?)
07-Dec-19 08-Dec-19 1 Matsue:
08-Dec-19 09-Dec-19 1 Okayama:
09-Dec-19 18-Dec-19 9 Kyoto: Nara, Himeji, Osaka, Kobe; 1 Night = Koyasan
18-Dec-19 20-Dec-19 2 Nagoya: Magome & Tsumago
20-Dec-19 21-Dec-19 1 Fukui
21-Dec-19 23-Dec-19 2 Kanazawa
23-Dec-19 24-Dec-19 1 Shirakawago
24-Dec-19 25-Dec-19 1 Takayama
25-Dec-19 26-Dec-19 1 Matsumoto
26-Dec-19 28-Dec-19 2 Yamanouchi
28-Dec-19 12-Jan-20 15 Tokyo: Kamakura, Yokohama (Half); 5 Nights = Mishima, Izu, Hakone, Fuji
12-Jan-20 13-Jan-20 1 Nikko
13-Jan-20 14-Jan-20 1 Aizuwakamatsu
14-Jan-20 16-Jan-20 2 Sendai Ginzan Onsen
16-Jan-20 17-Jan-20 1 Hakodate
17-Jan-20 18-Jan-20 1 Noboribetsu Onsen
18-Jan-20 27-Jan-20 9 Sapporo: Otaru, Jozankei Onsen; 3 Nights = Niseko; 1 Night = Biei/Furano (1 Night)