I know once we start digging into the rehab, there will probably be some big issues.

Also, FHA short sales issue a ATP with a designated NET proceeds required.

One issue that the owner has brought up is that sometimes he has trouble filling the 4th unit, but said that is primarily because his daughter, who manages it for him, isn't always diligent about advertising it. 

The contract becomes an issue when the parties start to disagree.

I can't speak for others, but the only time I see these types of issues being brought up are from people that have a financial interest in doing so.

You can create a separate "Overhead" Class for those transactions that are not house specific.You can then do reports "by Class" to see the details for any particular house.I have one QB file that I've used for over 200 projects...no issues for either me or my accountant.

I wonder if I have to wait til the 11th to issue the detainer warrant?

The big issue comes in with the repayment clause on the loan if you lost the job, as it would put you in a cash call type position.Ideally you would use the money on a down payment on a BRRRR scenario- and then when you refinance you repay the loan balance.  

Or are there some issues I may be looking over?

I would be more concerned about 'issues' than a particular score.