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Transport

Tokyo Metropolitan Area Rail & Road Atlas/English/Japanese
This atlas includes both rail and road maps for the greater Tokyo metropolitan area, with place names given in both English and Japanese. Immediately adjacent areas are also shown, such as parts of Chiba, Tochigi, Ibaraki, Saitama, Yamanashi, Kanagawa, and Saitama prefectures as well as cities like Mito, Tsukuba, Omiya, Urawa, Kawasaki, and Yokoyama.

Overview
A broad overview of the transport system in Japan.

To and From the Airport
What you need to know to get from the airport ot the city.

Automated Rail Schedule
English versions of 3 automated rail schedule database ranked in my personal preferences. The first (and better) is provided by JNTO; the second is provided by Jorudan. The third is Hyperdia.
If all these do not work, use the Japanese version in the Other Rail Resources section.

Bullet Train Overview
Exactly that.

Subway Overview
Exactly that.

Other Rail Resources
Resources from the WWW. Includes tips on travelling on the train system as well as automated rail schedule database in Japanese.