Army Heritage Education Center
Many aviation-related records from WWII are held by the Army Heritage Education Center and Military History Institute at Carlisle Barracks, PA.
This center is an excellent resource for anyone trying to research WWII (and earlier) histories, photos, etc. for many fighter, bomber, and transport units since the USAF wasn't formed until after the war.
Search engines available at
http://www.carlisle.army.mil/ahec/index.htm can help you pull up bibliographies for specific types of units, aircraft, etc.
Contact links are also available on the website for research assistance.
Obviously, Navy and USMC archives are held by their respective museums/history centers. The new USMC museum at Quantico, VA is a superb resource.
There are also a number of 'coffee table' books published on specific aircraft that you can probably get on an inter-library loan. These may help you frame a question for the archivists at Carlisle or other history centers if you need assistance.
Good hunting!