Considering pideon feces and such can be a biohazard, and depending on the degree of dirtiness, you may be best off calling in a professional company like ServPro.
Boards will have soaked up ammonia and such, so any floorboards or wall boards need removed. Studs and beams should be painted with a product like Kilz which inhibits mold and covers smoke and water damage. Make sure the remaining surfaces are cleaned and sanitized, then put down floors, walls, ceiling, lighting, etc. as you would any reno project.
Depending on the type of floor that you have, you can sweep, wash or disinfect to get rid of the smell. Get rid of anything that is not in use to create space. You need to clean it on a calm day to prevent the dust from going everywhere.
Id use water and detergent and an old broom. Just hose everything down and squirt some dishwashing detergent down and scrub everything down. It may take time and elbow grease but with some hard work it can be done. Just make sure everything stays wet to keep dust down.