If you do cull, send a couple for testing - this way you know what your dealing with. Your state lab can also advise on how best to disinfect.
Generally - all bedding would need to be removed - most respiratory diseases are transmitted through feces, dust, dander, feathers and can linger on surfaces for periods of time - some are a bit easier to control/eliminate, but you would want to do a thorough deep clean. It may be best to burn the bedding if possible - but again, it depends on the illness you have.
I'm not trying to be vague, but there's so many possibilities - getting more information on the specific disease you have - then studying how it's transmitted, how long it lasts in the environment, etc., would be best way to proceed in your clean out/sanitizing, waiting period and start over.