Japan National Tourism Organization has launched a website for muslim visitors to Japan.
They list hotels and restaurants from all parts of Japan that are muslim-friendly. Very helpful. You can also check travel reports by two muslim bloggers. PDF version is downloadable from the top page.
The previous printed version was quite disappointing since perhaps 90% of the restaurants listed were not Japanese. This time there are more Japanese food restaurants. You can see how much Japan is changing with the increase of muslim tourists especially from the ASEAN countries.
Also, they have a youtube channel!!