I do have a property manager, and they added up all the repairs, last month of rent, time spend off market fixing the place, and send them a final statement once deposit was subtracted.

With two vacancies and the owners house not rented, and the rentals bringing in $11K, we would be at a 0 or negative cash flow by the time we subtract the HELOC payment.

If I was you I would let the seller know you are intending on buying the house to rehab and flip for a profit and that the deal will only work for you if the property is acquired by you for less than market value, then let them be the first to set a price, then you either accept knowing it is well below market value and at or under your max price you accept if not than you start the negotiation by telling them the most you can spend is X and that includes the rehab costs which you figure to be around X so subtract that from the max you can spend and that is what you can offer the seller.

Running the numbers simply means calculating the income and subtracting the expenses.The fancy term for this is underwriting but essentially you're trying to estimate how much you will make from this property.You'll want to estimate- Taxes- Insurance- Maintenance- Utilitiesthen subtract them from your potential income

However, since this was used on your investment properties you can subtract it off any rental income you had.

You'll probably have to subtract from that gain some negative cash flow (10% down may make cash flow off the bat tough), and you can add some back in for tax benefits and debt reduction, but the wealth on your balance sheet grows fastest this way.This is not to say 10% down and negative cash flow is good. 

Note this does not mean I make the full rehab cost because holding costs have to be subtracted.  

Wondering, based on this overview of our strategy, what would you add or subtract to optimize our time?

Its more work up front and it requires me be constantly adding and subtracting but I have more control of my contractors that way.

In the absence of either of those, I would use SFH and subtract for the smaller yard, reduced privacy, etc that impacts your ADU.By the way ADUs in southern CA are often one of the worse RE investments.