I used Inside Japan tours in 2008 and I am using them again this year. I love everything about them. I do the self guided tours, which are the best I think. They talk with you through the entire process, and if the price seems high they work with you to help lower the cost. You basically tell them where you are interested in going and they send you an info packet 1 month before your trip with all the different ways to get to where you want to go laid out.
If you have problems they have a Japanese office you can call while you are there and they help fix any problem you might have.
I would highly recommend Inside Japan Tours
