This has made me a little nervous and I am being told that the delay has been because they have to separate some other business dealings from the numbers, and that the son of the seller is their financial advisor and accountant. 

If you don't have equitable assets then your risk is minimized and an LLC is not needed.

It is now a good cash flowing property that we used minimal down and were able to live in.

@Craig GordonWhat you are referring to is called a "Delayed Financing" or "Technical Refinance".Follow this link: What Is Delayed Financing For Cash Deals?

The greatest impact that low rent did was delay the time to profitability on this property for quite a while. 

Other wise you get into a situation where a partial payment will delay your ability to start foreclosure.

Minimal debt (nothing so bankrupting as student or medical debt), currently a low cost of living, and the job I have at the moment pays well. 

And you're right about the flood zones, very minimal to zero flood zones in Indy.

You seem like someone who has kept it well-maintained, which should minimize the need for excessive repairs and allow you to set aside more of that 50% rule money towards future cash reserves.It sounds like it's in a good, rentable neighborhood.  

I've read IRS auditing guidelines (they're on their web site) and these specifically state that managing rental properties should be assumed to require minimal time.