The essential single source reference on this subject is still The Japanese Air Forces in World War II (The Organisation of the Japanese Army & Naval Air Forces, 1945) published by Arms and Armour Press in London and Hippocrene Books Inc in New York in 1979. (ISBN 0-88254-492-6).
It is in fact a reproduction of a detailed intelligence analysis of the Japanese Air Forces published by HMSO and contains a wealth of organisational information and glossaries of terms.
You will find many copies available through Abe at:
http://dogbert.abebooks.com/