I can't speak to everything on your list; as I'm a small scale miner.
One detail people may need to know is are you planning on building a new facility or modifying an existing building?
Here is a thread to give you a decent jumping in point regarding mining.
First time/Small miner reference for getting started.That topic will go over the basics and give you insight into how you can estimate your power consumption. Also consider following the link to competitive hardware.
Security - This will depend on the country you are operating in as well as the location urban or rural. Personally a secure facility with the minimum amount of doors and no main level windows would be best. You can then get a monitoring system for security that notifies the local police in case of alarm. These are handy, but false alarms do become burdensome. The thing is your facility is more at risk of being mistaken for something else with an easier to move stolen goods.
Tools - Again I'm not to sure but generally you will be responsible for your own transformer(s) and electrical infrastructure. You will need/want racks obviously to position the miners and PSU's. I would assume you will also be investing in PDU's; at the level your talking you may want smart PDU'S they cost a substantial amount more but offer features you may find useful for switching and power consumption monitoring.
Airflow -Look up Hot/Cold aisle. This will have your miners with a wall essentially running down the middle. Ambient intake air on the miner intake side and the hot exhaust coming out the other. This is also how you will handle the cooling using intake fans for the cold aisle, and exhaust fans to discharge the hot aisle. Do not use AC it will kill your profits.
Not sure what you mean about storage. In regards to spare parts, you will want to have spare PSU's and PDU's on hand. that way you are set for a quick swap if one craps out. If you use Avalons then I sould suggest a spare Pi or 2 (controllers for up to 20 machines). I would also hold onto any machines that do go down as there may be some interchangeable parts you can salvage - Fans, Hash boards, Control boards, Cables.
Good luck, maybe someone with more experience in the larger centers can give you some specific ideas for sizing fans.