[StueyT]

As for hostels, in my experience these are good stays...

Tokyo:
K's House, Asakusa (Very close to Asakusa landmarks, very easy subway links to all parts of the metropolis)

Hiroshima:
J-Hoppers (Very close to Peace Park)
Backpackers Miyajima (Next to Ferry port for Miyajima)

Kyoto: J- Hoppers (10 mins from Kyoto Station, walking)

Osaka: J-Hoppers

Fukuoka:
Guest House Kaine (Old Japanese style hostel, very very very friendly owners and has an integrated Udon restaurant)
Khaosan Fukuoka (nr Hakata Station)