We have in Japan some organizations who provide accessibility travel infrastructures in Japan. The two major sites are:
Japan Accessible Travel Organization (日本バリアフリー観光推進機構)
Japan Universal Tourism Promotion Network (日本ユニバーサルツーリズム推進ネットワーク) http://jutn.net/
By utilizing these organizations, you can reach to a lot of regional organizations are there in Japan to support you. Japan Universal Tourism Promotion Network offers information only in Japanese as of today, we believe they can support travel needs of non-Japanese speaking guests with special needs. So do not hesitate to contact them for information.