No doubt you will continue to have exterior lighting, possibly hall/stairway lighting, hvac or water heater on either one or both of the two panels you currently plan to split. 

I have had to go directly to the plant to work out fixes for things CAD overlooked such as missed point loads and stairway clearance.

You can require the animal is leashed or in a carrier on common areas, in particular elevators, stairways, and hallways, unless doing so prevents the animal from performing it's task.

It may be best to market it as 12.5 feet vs 13.You say good location--but less than optimal layout.If it's an upscale area (or a wanna-be upscale area) maybe put in a minibar and doll up the stairway using stripper and whatever...Also if you have another 3 or 4 feet in front of the front door--and have the ability to push the front wall out into an \____/ maybe you could add some side windows plus some sq ft.And glassing the end with a big patio door might be unusual, but might also make the unit feel larger.Being it's an out of the ordinary layout (shotgun shack) and in a good area, something like in pic (1) might draw a different type of renter than your standard apartment unit--a little more upscale...but that adds risk to the mix too...as these people may not be as plentiful as section-8.It all depends on your business model.Just some food for thought.Good Luck!

Further, you can also place "reasonable" restrictions on the animals, including the requirement of a recent veterinarian report on the health and vaccine status, with annual updates; must be spayed or neutered unless contraindicated by veterinarian; must be in a carrier or on a leash (unless this prevents them performing their service or task) in common areas, especially elevators, stairways, and other areas where people would be in confined spaces; must clean up after the animal properly in common areas; offensive odors must not emanate from the residence; aggressive or nuisance behavior (such as extended periods of barking NOT related to the service or task they provide) can be prohibited, and potentially grounds for removing the animal and/or the resident; animal must have a chip or collar with owner's identifying/contact information; must have appropriate city/county license if required locally; and photos of the animal for your records.A thorough and clear policy will deter many of those that are less than sincere from applying when they are made aware of the policy details early in the process...like at the viewing, and mention of the policy in ads.

I might offer to ignore the fence encroachment for now in exchange for ingress/egress via the prior permissive use until the new stairway is complete.

If so is a stairway as a means of egress to the outside required?

If you redo those steps - yes the inspector will expect the stairway to be code and there is a height from steps clearance requirement.

Spiral stairways are permitted, provided the minimum width shall be 26 inches (660 mm) with each tread having a 7 1⁄2 inch (190 mm) minimum tread depth at 12 inches from the narrower edge.

There is also common area repairs I want to do: a couple of new water heater, new carpeting on the stairway, paint, etc.