Hey guys,
I've been living in Japan for a bit now and have also been on a search for Fukuoka inspired farms - but have yet to find any. I did a bit of Wwoofing some years back and we searched out and visited those farms that practiced natural farming (none of the farms in the Japan WWOOF directory even mentioned Fukuoka-san). We did find some nice farms but the methods and principles weren't quite what we were looking for.
I've been growing Fukuoka's Happy Hill rice for four years ago and have tried unsuccessfully to duplicate his methods. After the first two years I felt that I had learned enough to possibly have a chance of success but each year some random problem would arise and wipe out the crop. I would agree that the few Japanese who know of Fukuoka-san believe that his methods are too difficult to replicate and prefer to follow Kawaguchi-san.
There is a farmer near Fukuoka city, Takao Furuno, who has developed a very effective, permaculture-like system of duck, fish, and rice farming. Although he uses machines his methods are duplicable without. His runs a very successful farming business and his ideas have spread into parts of Asia.
Also, this film looks like it will be worth watching
http://finalstraw.sociecity.com/index.html