An alternative is to screen them for good pet ownership (fill out a separate pet application) and charge pet registration fees and pet rent.

But those have all changed to separate recon docs.

So you might have thought it would cost $20,000, you can stand there and say I'll give you this work for $5,000 and materials are separate, that guy knows he'll be busy for 3-4 weeks at a set rate.

How do you separate tasks?

I can tell you that it is best to always have the option to buy the house separate from the lease. 

Do I setup separate accounts for each property?

Should we view each unit separately or just view the duplex as one property since it’s under the same roof?

We each did one separately this last fall and those worked out well.

Upper floor has 3 bedrooms and a bath and lower has a separate entrance with suitable space to make into a 1 bed apartment.

I believe most of these other items remain grandfathered, though I'm assuming you mean by "fire doors", doors that are supposed to be used for fire separation, and not a separate means of egress (because those are usually required).