The issue is that a lot of issues popped up on the inspection.  

My plans is to stay within arms reach of my home (Paramus) so that I can manage issues the may arise

The only issue with that  is that it will make it more difficult to sell them individually in the future.  

I want to make investments I can repeat so this method doesn't seem to solve that issue, just cut it in half.

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.