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traveling Japan for 2 months--cities to base in?

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I am traveling Japan for 2 months and am hitting a lot of cities. Therefore, if anyone can help by telling me what "base" cities to stay in and what places are reachable from those bases? For example, I would like to visit Kyoto, Nara, Mount Koya, and Himeji. Thus, I have been told I should book a hotel in Kyoto and take side trips to Nara, Koya, and Himeji. In addition, what would be the best route to take to visit all the cities? I have tried my best to figure out the routes and staying accommodations but am having such a difficult time! Any help would be appreciated. Thank you :)

My destinations are:
tokyo
matsumoto
himeji
takayama
kanazawa
nagoya
kyoto
osaka
kobe
nara
mt koya
hiroshima/miyajima
fukuoka
mt fuji
Ise
chichibu
nikko

and possibly if time permits:
matsumoto
kamakura
noboribetsu
hakone
okinawa
shirakawago
hachimantai
magome
yokohama
sapporo
nagano
nagasaki
sendai
kagoshima

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