Will JR Pass work for my itinerary?

I have a very rough itinerary drafted for a trip in late October through early November for 12 nights.

Arrive Narita Airport > Tokyo 4 nights > Kamakura day trip > Kyoto 2 nights > Nara day trip > Osaka 1 night > Himeji day trip > Hiroshima & Miyajima 2 nights > Kumamoto 2 nights > Tokyo travel day > Narita Airport 1 night at 9hours capsule hotel, then departure.

Again, this is very rough, I'm just trying to figure out if JR lines connect all these places at this point. Then I'll be able to decide what is most cost effective.