The directions in the Lonely Planet Hiking in Japan guide can be very good, though I always check publication dates on books like that and I don't think that one has been updated in awhile. Still, we used that book to help us hike from the Silver Pavilion to Nanzen-ji in Kyoto a few years ago and it helped with all of the numerous intersections in the woods. It's at least a good starting point for ideas on trails in certain regions.
I've been hiking here for 15 years and haven't really found a comprehensive guide I like yet. There's a lot of info on individual hikes on the internet, but it's mostly in Japanese. So I'm putting together individual English articles of my own. Hiking Mt. Kaya and Mt. in Fukuoka here.
I would suggest using a variety of sources to get the best inforamation. The blog listed (japanhike.wordpress.com) is good, but often there will be hiking information listed by a Japan-run site.
For example, do a google search of the specific place (once you decide on it) and you can find sites such as this: www.oze-fnd.or.jp/en/rg. That one is specific for hiking in Oze National Park in the Kanto area.
I just hiked Mt. Shibutsu a few weeks ago in Oze, and I highly recommend it! If you need more info. on that, click here!