I started thinking about biking down Japan quite a while ago, while I was at the University of Nevada in Reno. After the school year ended, I had already planned on going to Hokkaido for a friend's wedding around the end of May. The wedding was in Niseko, a tiny town known for getting sh*t tons of snow in the winter, but fairly quiet in the summer. As fate would have it, there was a guy biking up to the wedding from Tokyo (on a freakin mamachari) so when he got there I started to ask all the questions I had about cycling through Japan. I was pretty easily convinced to do the trip, so I bought a new touring bike (and yes its not cheap) and set off to Okinawa. My luggage included a tent, sleeping bag, pad, clothes, cooking pot and fuel, rice, clothes, repair stuff/necessary bike sh*t, and a six pack of beer. Other than that it's all small stuff.
If you're thinking about biking through Japan I would try to find someone who's done it before but if you can't no need to worry. Lots of people tell you lots of different stories about what you should and shouldn't do, but the main point is that Japan is really, really safe.
And PS I was kidding about the beer. This is my first go at writing a blog so if you made it here more power to you, and thanks. I'm currently in Yui, a town about 25 kilometers east of Shizuoka but if I get to it I would love to write about everything I've encountered so far (such as old ladies selling cooked mochi, 4am encounters at a bar, and "the brew". More to come.