If I started an LLC and used NAICS code 531390, the IRS would keep a closer eye on my company and I have a higher likelihood of being audited VS. me not having an LLC...

Do a search on here and you will find some posts.

The first is renting out my house to a company that, will in turn, rent it out in a mix of MTR and STR.  

As long as your insurance company is good with it, I think it's an excellent addition. 

We partner with a third-party management company who handles all cleaning, maintenance, etc. 

Hello, I recently started a property management company and currently manage around 80 properties.

The degree of how much will vary from company to company, but it'll be a cliff-like change in their financials to operate under this cost of capital. 

I recently did the same and used a company called Ubiquity. 

I once bought a school from the county board in which there were no disclosed leases on the property only to find out later that they failed to disclose an internet company was leasing a small shed (probably 4' x 6') on the property.

To answer your question directly though, to move the ownership of a property to an LLC we usually go through a title company to help with that.