Looks like you'll be in the same boat as I am. I'll be arriving in Japan on July 3rd for 2 weeks. Except I'm pretty lucky cause my uncle lives there, he teaches on one of the army bases, so I can use his house for a homebase. I'll be going to Tokyo with him cause he knows it pretty well, plus he's eccentric so he'll be able to show me some cool places.
After that I'll probably take off for a couple days at a time keeping what I need in a hiking backpack and travel since I picked up a two week Jalpass. Yup every few days or so head back to his house and restock and take off again. Also my Girlfriends currently there studying so I'm set cause I'll see her on the weekend.
It is a good Idea to buy a book or two, and also a map of the country. Hopefully my preparation will pay off.
Have a good time and best of luck