What is the minimum that I can borrow using a conventional loan ?

Hi Raymond,Consider using a 3.5% FHA loan or a 5% Fannie Mae program, as these options are advantageous if you plan to live in the property.

What are the downsides of using a HELOC?

It's worth consulting a local attorney or using a reliable legal service to ensure it complies with state and local laws.

I had to prove I had 20% down and I used and all cash buyer then I bought it from using a 30 year mortgage.

If you mean you are using a "Construction loan" to add onto a SFH adding 3 units that could work but you still need a down payment. 

. - Conventional purchase with 20% down using a HELOC: Current cashflow from the SF could cover a big portion of the HELOC payment, but this starts to feel risky from a cashflow and funds available for rehab.- Conventional and move there/rent out my primary: Certainly the best option, but a hard no from my S.O.'

Consider using a holding company structure for centralized holding and additional asset protection.

Seems funds would be available quicker using a checkbook with this structure. 

@J Scott, it looks as though you're using a Desktop version of QuickBooks.