depending on how your brewery is set up, the debt on it may hinder your ability to purchase.

As silly as it sounds, there are a million reasons for someones' discomfort when investing but that same discomfort sometimes will forcibly hinder the potential for their true success.  

So I'm willing to do refi cash out (investment mortgage much higher) for my present MF to get down payment for the upcoming #2 - (3 unit), but that causes my Loan to Income ratio to rise and hinders the #1 owner occupied pre-approval

If not moving hinders your ability to achieve your goals or objectives, you move.

If I wasn't doing a rehab, i would definitely get my financing up front as long as it doesn't hinder the opportunity to acquire the property.

From a sales standpoint this really hinders your ability to sell.

You can go the HUD route if the CIty wants to but that may even hinder the value of the property depending on what the developer wants. 

There are a number of practices that can help defer taxes or help get preferential rates, but real estate has been bought and sold for at least a few thousand years before anyone thought of the United States or the IRS, so it's fairly well understood and they generally will make sure that tax is paid on income earned in this space.You'll want to figure taxes into your planning- the way you structure your business may help or hinder you through when the income/appreciation is recognized.

In regards to the rules you are speaking of, which "certain rules" do realtors have to follow that you think would hinder them when it comes to actual investing? 

On site they have 3 units (1 unpermitted).My first question is by one of the units not being permitted will that hinder me in any way or can i still rent it out to someone.My second question is in the description for this complex is says the property is currently in REAP what does that mean as well?