Maybe let her know it's a fire hazard or safety concern or that if you get inspection from the fire department you could be looking at a huge fine. 

Many things go wrong in construction, some of which are unavoidable, how the contractor handles those issues is paramount and speaks volumes to their abilities (or lack there of in the cases above).There are no short cuts to construction or dealing with the building and safety/planning departments in cities, they are slower than turtles in almost all cases.

Here are some specific questions I have, but any additional information is welcome:Safety and Community Feel: How do locals view the safety and overall community vibe in Pine Hills?

If it’s a safety issue, I’ll of course make sure the premises are as safe as they were before any required maintenance was done, but she is now suggesting that if I don’t reimburse her for those specific anchors, I am violating fair housing laws for familial status and/or tenants rights regarding not incurring costs for required repairs.

A landlord does not need to provide a reasonable accommodation for an emotional support animal when:The property is an owner-occupied building with four or fewer unitsThe property is a single-family home sold or rented by the owner without the use of an agentThe emotional support animal poses a risk to the health or safety of other people, or a risk of substantial damage to property (but this risk must be specific to the animal and cannot be based solely on assumptions about the animal’s breed)"Definitely have a chat with a local attorney to ensure your local laws apply, nonetheless since its an owner occupant, it sounds like you have some recourse to deny this request. 

Keep your personal safety and that of your tenants and neighbors in mind. 

Ultimately I am worried about protecting our business's reputation, the safety of our tenants, and having a viable rental. 

Now a landlord (and architect), I wouldn't build out the space without the second stair since it really is a safety issue/liability (especially in case of a fire) if anything were to happen.Full excerpt of building code below:According to the Chicago building code on egress requirements, the third story above grade plane within a dwelling unit [which in this case is the duplex-up unit], all the following conditions must be met:1.) the building is equipped throughout with an automatic sprinkler system2.) the floor area of the story does not exceed 1600 sq ft3.) the dwelling unit has an exit that discharges directly to the exterior at the level of exit discharge.Your third story attic space is unlikely to exceed 1600 sq ft, but you'll probably find the sprinkler system to be cost-prohibitive.

I am risk averse and if I were to purchase, I would tear down to the studs and do a full rehab {this would include getting rid of asbestos shingles and insulation).1) I have done a ton of research and it appears as if getting rid of asbestos is very DIY able assuming you spend money on the safety equipment and use it properly. 

I say that no XX year old house is perfect and I will get any health and safety issues addressed but we need to be reasonable, we are not buying a new home.