Quote "manure does get collected for biogas supply".
I believe your posting has right now to many questions to solve at once. For safety issues, i would focus on collecting methane gas in a safe manner. Google "collecting methane gases".....BTW, clean hay (i heard dry hay) once it's ignited the fire rapidly takes off and no fun in trying to put that out...ask any fire person trying to put out brush fires--> I woudn't store dried out hay in a methane collection facility

we do have an existing bio gas pipe set up from the cow shed slurry and the rubber sap plantation (the agri dept provides expert help)…but since we are tearing the place down and rebuilding the shed on another side of the farm, i would like to do it properly giving emphasis on hygiene

My gut feeling is that you NEED pro's on site in order to solve your dilemma.