There are some exceptions: if landlord can prove it causes undue financial or administrative harm to landlord; the animal is a direct threat to the health or safety of others (bodily harm)...

And all of that can be done by a 1031 Exchange administrator of course...but that's if he wants to defer his long term capital gains taxes.  

For lower-cost properties, such as a single-family house at $200K, the benefits of having a separate LLC might not outweigh the administrative and financial burdens it incurs.

Mark, I have myself, my wife (owner payments and bookkeeping), a second property manager, and an administrative assistant.

VA administration has a great website with a lot of details about the program: https://www.benefits.va.gov/homeloans/@Alan RezaNot 100% what checklist you're talking about, but send me a message.

However, I'm interested in more detailed guidelines regarding the specific categories of expenses and income, as well as any operational assumptions you might advise.For instance:General and Administrative Expenses: How do we determine if costs related to software, credit card fees, office supplies, etc., are reasonable based on the size (square footage) of the facility?

Check with your plan administrator for details.

I would mention the fact that your neighbors are ok with your renovation and that the administrative nightmare is causing you and your family financial harm. 

This can significantly lower your initial payments, making it easier to manage cash flow before your business starts generating income.SBA Loans: While typically requiring business revenue for eligibility, some Small Business Administration (SBA) loan programs are designed to help new businesses get off the ground.

Florida Statute 162.09(3) provides:Chapter 162 COUNTY OR MUNICIPAL CODE ENFORCEMENTSECTION 09 Administrative fines; costs of repair; liens.(3) A certified copy of an order imposing a fine, or a fine plus repair costs, may be recorded in the public records and thereafter shall constitute a lien against the land on which the violation exists and upon any other real or personal property owned by the violator.I handled multiple title insurance claims where a CEL against one property was missed in a title search for a different property owned by the same party.