We used a comination of rail and car travel outside of the urban areas e.g. Kamikochi. Public transport is fantastic and driving within urban areas is not recommended but gives greter freedom in rural locations. We did alot or research in advance to plan our route, but JapanTravel were fantastic in making most of the arrangements and answering all our questions. We even has some on the ground support from their local representative in Fukuoka which was completely unexpected and very very helpful. We recommend Japan Travel highly.