For anyone in my shoes would you take it to small claims or collection agency?

In your case, as others have mentioned, you can transfer the property out of your name into the LLC via quit claim, but not the mortgage.  

And supplies from Home Depot.In the event that I'm audited, would my credit card statements and copies of the checks I wrote to the contractors be enough to support my expense claims?

You, as the agent, are open to a claim for fraud for anything your boyfriend misses. 

Today the title company sent the seller and me the HUD statement and the seller is claiming she never agreed to $2,000 towards closing.

what is good for long term where I definitely will have profit every year on my rental even after claiming depreciation. 

I kept the security deposit to cover some of the unpaid rent, and rather than file for eviction and claim the rent that I was due, let them off the hook for about $1,000 in unpaid rent.

They claim that they focus on the development of the building, not the management and that's why they aren't organized on receipts, better financial reporting, etc.Am I just being paranoid here?

If you quit claimed it instead of a warrantable deed, they will attack the chain of title.

There has to be a water meter, even if it is one master meter for the entire property.I would check that meter against what the utility company claimed was the last reading and pro rate the usage.