The Riding-
I found Tokyo and Osaka awesome to ride around in, don't bother riding on the paths it can get frustrating even though people typically get out of the way when you ring a bell.
Ride on the roads, I felt safe, especially in Tokyo as the drivers are careful and courteous.
**Kyoto was a different matter, the drivers are aggressive and awful, ride on the roads defensively and at your own risk. **
double eek!
http://www.kumocycles.com/japan-bike-guide.html