Two week itinerary, from Tokyo to Kumamoto

Hi there, I'll be in Japan in April, 2015.
This is my plan:
9 Narita - Tokyo - Kumamoto
10 Kumamoto - visit to Beppu
11 Hiroshima
12 Hiroshima - visit to Miyajima
13 Kyoto
14 Kyoto - visit to Nara
15 Kyoto - visit to Osaka
16 Kyoto
17 Matsumoto
18 Matsumoto - visit to Takayama
19 Tokyo
20 Tokyo - visit to Kamakura
21 Tokyo - visit to Yokohama
22 Tokyo - Narita

I need your help about a few questions:
Is it possible to take shinkansen from Narita airport to Kumamoto?
May be all of these destinations reached by JR trains (I ordered a 14 days JR pass)?

Thanks a lot