I have paid off most of primary home so broker is not able to do re-fi (~212K) at lower rate with no point no fee loan.

Sure, and we might all be just a dream in a giant's head. 2.

My roofer said its better to just go over it, and if I rip it off it will cost a hell of a lot more money, not to mention open up a giant can of worms.  

Zillow is not your local expert, it is a automatically generated giant who gives people false information on the value.

It might mean that you end up doing a partial 1031 Exchange because you were not able to complete the entire project and you end up trading down in value or not reinvesting all of your cash equity from the sale of your relinquished property. 

I'm not able to think of even one 100+ unit in the market.  

Since I am just starting out flipping single family homes, I have no documented experience or homes as collateral so getting a giant amount of money is unrealistic.

The house is located in an area that’s conducive to short-term rental (which is his long term plan with the house), but he’s not able to use it as a shot-term rental while he’s restricted from moving into it because he financed it with a VA loan.

if you need a giant dragon in your back yard made of fiberglass and fire coming out of her mouth or 15 ft Naoh's Ark made of all wood for your church / school , I'm the guy..  

If you are doing this all in "cash" using the SDIRA - then you are not able to refinance that money back out taking title in your personal name the long hold - tax laws.