We are still operating it as a short-term rental.

These taxes are typically split 50/50 between seller and buyer, but you can write it into the sales agreement if buyer is to pay the transfer taxes.

Otherwise, people in that price range typically have their own furniture and want to use it. 

I think it is the type of mistake that is made and how the accountant deals with you bringing the issue to him/her.I think the accountant should be doing atleast a bring overview of the documents / information that you provide.At the very least, when clients bring me their Profit and Loss, I try to see that they have the typical expenses that I would see for real estate investors and to see if the numbers make sense.

He told me he's the most expensive guy in town but gave me pricing for the typical roofer around here...

We operate quite a bit in Berwyn, Forest Park, Cicero and the surrounding western suburbs, and I can tell you each town has its own way... 

My own criteria is a minimum monthly cash flow after debt service of $300 on a typical B class SFH.

If they are coming on as partners with ownership rights instead of lenders, you would likely have an LLC operating agreement or JV agreement that dictates everyone's roles and responsibilities. 

With a clean-out like this I typically take anything usable to the Salvation Army as a charitable donation.

Typically it is 24 hours' notice.If they are still in the place and don't pay rent Feb 1, start the eviction process.