I won't explain the details, but I have extensive experience with bureaucracies and base my advice below on this experience.
1. Adopt the Socratic method. Answer questions with questions. Do not commit to any description of reality made by others (as much as possible).
2. Understand that the highest levels of leadership are political appointments and they promote their patron's interests. eg: Does your brother-in-law know the dept. mayor's wife? Explore your network of friends and family for political influence.
3. When you write: "Now, I do not know about the titles and hierarchies involved in the county organizational chart," I very much feel you need to hire a lawyer that specializes in these kinds of disputes to advise you. Not necessarily take legal action, but to explain your options. The bureaucrats will know the rules well. You need an expert on your side.
4. Use these words, "What would you do if you were me?", when you find yourself at a road block. Also ask questions like "has your office ever issued a waiver for [problem]?" and "who has authority to issue the waiver?"; naturally followed by, "may I speak with this person of power?" The answer will be no, so you should ask questions like "whom does the person of power report to?" You won't get instant solution, but things will start moving behind the scenes.
The bureaucrat's goal is to get you to accept their 'no' or 'wait and see', so you will go away. Your goal has to be acting nice and reasonable, but persistently questioning the management of the process. It will become easier for them to get you in compliance than continue to deny you.
Sadly, this adds much delay and expense.
Best of luck to you.
All of these problems would have been conveyed to the business owner, avoided altogether, or could have been mitigated some other way.
It's a shame, because usually a competent building owner/manager will usually inform a new tenant that they should or demand the use an architect (especially when poking holes in roofs).