Here are a few resources to help you sort out driving in Japan. Check them out!

How to Get a Japanese Driver’s License (Guide)

If you need to get your Japanese Driver’s License, check out these guides that have been put together by your fellow JETs. They cover the process for getting a license, what you’ll need, and so on.
Japanese License Overview
Driving Strategies
Driving Course Notes

The Ino Driving Center

This is where you need to go if you need to either get your driver’s license, get your license renewed or if you have any other issues with your driver’s license. The address and phone number can be found on your right.

The General Information Handbook

The GIH has a lot of helpful information about the process of getting a Japanese licence, as well as driving in Japan, on pages 125-127. Give them a read!