Itinerary and JP rail pass

Dear Daniel San,

Could you please help me? We'll visit Japan 3 weeks in October. I'm not completely sure about our itinerary, but it will be something like this:

Tokio
Hakone
Tsumago
Kanazawa
Kioto (Nara/Koya San/etc)
Naoshima
Hiroshima (Miyajima)
Fukuoka/Nagasaki?? (maybe)
Osaka?? (maybe)
Tokio

I think we'll be in trains more than 14 days, but can we travel everywhere with the JR-rail pass, or do we need other tickets as well between certain cities? For example between Tokio-Hakone-Tsumago-Kanazawa - can we travel there with the JR-rail pass? Or should we buy a 14-day pass and then buy some other tickets seperately? I hope you can help us!

Many thanks,
Maria