Need help choosing passes

Hi, we will be traveling around japan for 5 weeks, but will only use trains for part of the trip:
2.04 - Narita airport
7.04 - Tokyo - Hakone (Odawara) - Tokyo
9.04 - Tokyo - Nagano - Yamanouchi
10.04 - Yamanouchi - Kanazawa
12.04 - Kanazawa - Kioto
12-19.04 - Kioto - Nara, Kioto - Osaka, Kioto - Himeji, Kioto - Kobe - not yet decided which day for which city
19.04 Kioto - Hiroshima
20.04 - Hiroshima - Miyajima-Hiroshima
21.04 - Hiroshima - Nagasaki
I got a little lost trying to order passes, could you help me please?
ewa