I know it's kind of a "crap out" but get the book
Japan from the Lonely Planet series... it's an insanely comprehensive book with accommodations, sights, and highlights (including festivals), all the while explaining how to get to and from.
Hostels in Japan are probably better than Hostels in Europe- considering the Japanese are masters of little-tiny dorm rooms.
I suggest Sakura Hostel in Asakusa... it's in a great little area within a 2 minute walking distance of Senso-ji temple. It's cheap, has internet, and the staff speaks English and are around 24/7.
Indeed there are tons of threads on the subject of where to go... it depends on what you enjoy, but there are a few given:
Himeji Castle
Nara (And the Daibutsu)
Miyajima
etc. etc.