Japanese Shinto and Buddhism
If you are interested in shrines and Shinto (that is the indeginous religeon of Japan) and Japanese temples and Buddhism, I recommend you to visit Meiji Jingu (Meiji Shrine) and Sensoji Temple during your stay in Tokyo. I think you can get the feeling what they are like there. Your guide will help you to learn more about Japanese thought about these religions (Christianity may also be included in the explanation).
Following are English web sites of Meiji Jingu (Meiji Shrine) and Sensoji Temple:
*** Cycling Tour to Learn Tokyo Culture ***
If you are interested in a cycling tour to know Tokyo Culture, following site has useful information. The office is near Sensoji temple at Asakusa (81-3-5830-7769). 'Tokyo Culture Cycling Tour' . (search by 'Tokyo Culture Cycling Tour' )