A sketch of what my itinerary looks like so far..

edit: My new itinerary -

Day 1: Shin Yokohama > Beppu
Day 2: Beppu
Day 3: Beppu > Kumamoto > Hiroshima
Day 4: Hiroshima > Okayama > Kochi
Day 5: Kochi > Matsuyama > Osaka
Day 6: Osaka > Kyoto > Nara > Kyoto
Day 7: Kyoto > Shizuoka > Shin Yokohama

Wow, what a fun week it was! This is how it ended up turning out..

Day 1: Shin-Yokohama > Kokura > Beppu
Day 2: Beppu > Kumamoto
Day 3: Kumamoto > Kagoshima
Day 4: Kagoshima > Hakata > Hiroshima > Okayama
Day 5: Okayama > Shin-Osaka > Osaka
Day 6: Osaka > Kyoto
Day 7: Kyoto > Shin-Yokohama

I guess it was worth getting the pass