I doubt you will find a HELOC but there are other programs that may fit your needs like cash-out or bridge. 

I obviously don't know the contractor but those trades are probably being subcontracted out and he is adding money on top of that.

First guy did the framing for walls and layout of the basement, the door frame was too small for the door so it won't fit and he did the tile without cement under it.

This is a double edged sword, if things turn south it can be just as bad.Refinance is best used in growing market, on top of that the tenant is paying off the principal, So even if your cashflow is low you are increasing your equity each time principal is paid. 

I'm aware there are going to be some surprises, but I just want to factor in as many surprises as possible even with the budget, then have a surprise budget on top of that. 

Also with VA loans, if wrapping the fee into the VA loans, it can take a while to have equity in the property (we also refinanced for the low rates, which put fees on top of the fees which takes a while to pay down at the 30 year amortization). 

I am getting top dollar and my HA keeps my calendar full.

@Logan Allec I guess I am just looking for a perfect fit instead of just making it fit.

It's called a casualty loss, and those rules got more complicated with the new tax bill, you'll need to speak with a CPA to find out how it'll fit your exact circumstances because generally the casualty loss deduction went away in 2018.

The triplex was recently renovated and fitted to meet the needs of this type of property.