Just a summary of events for the general public:
Trip started on Sept 2nd, 2003 from SFO into Narita and ended Nov 4th from Narita to SFO.
On the whole I stuck to a pretty strict budget, sticking to cheaper salaryman type restaurants mostly and at times eating a convenience store meal. Then again, 8% of my budget was beer (see graph below). Exchange rate was close to 110Y/USD while i was there.
I had a 3 week rail pass with which I went through Hokkaido, Kyushu and Shikoku. Then I settled in Kyoto for 3 weeks and then Tokyo for 2weeks.
I used the 7th Edition (2000) of the Lonely Planet Japan Guide (The 2003 edition came out while I was there).
Overall recommendations:
Kyoto and the Kansai region around it has a bit more diversity than Tokyo.
In Kyoto, Jhoppers is an excellent place to stay.
Internet cafes are all over the place, but usually there is a cost (100Yen for 30min is on the cheap side). Some offer free service provided you buy something (tea or snack for around 500Y). In Kyoto, the British Council offers free internet service. They are located around Karasuma and Shijo on the 8F.
In Tokyo, the best place for free internet is the Yahoo cafe located in Harajuku. It's tucked on a side street back a little bit along Mejijingu-mae, SE of the subway station but before the pedestrian bridge. Another place for free internet is the Marunouchi cafe in Central Tokyo. There is a British Council location in Tokyo, however they don't allow you to check e-mail (although you are free to browse the internet..)