The Tokyo Metropolitan Government recently started Tokyo Business Entry
Point, a free "one-stop information portal for foreign-affiliated firms".

http://www.tokyo-business.jp

Quoting from the site:
"In addition to essential business-related information such as Licensing
regulations and governmental support services, this one-stop portal also
offers information about education, housing, and other day-to-day
necessities."

I believe they are still quite quiet at the moment so it is a good time to
be asking questions.