I did find a book in a Tokyo bookstore entitled "Road Atlas: Japan 1:250,000" -- English edition for Y3000, published by a company called Shobunsha. Not online but might help you if you can find it and are planning on driving when there.

It contains the useful and amazing fact that Japanese national toll roads all use the same toll rate: Y24.6/km, which means toll is about 32 cents per mile! No wonder the toll roads outside the major cities are so empty.