Get advice from OUTDOOR JAPAN website:
This is a magazine produced in Japan but written in English, with a great website: check it out for features on rock climbing, cycling, hiking, camping, surfing... you name it, someone has done it, written about it, taken the photos and can offer you advice.
Amazing walking tours from HIKE JAPAN:
This is a niche tour operator with the most remarkable walking tours in Japan. Some are strenuous, for the serious and fit hill-walker only. Others are more leisurely. Tour groups are operated with 5 - 8 participants. Accommodation is mainly in traditional inns, hostels and temples. You have to arrange your own flights. See the whole range of tours on their website.
[Links to both on the left]

