Whether a buyer paid all cash, had owner finance, bank loan, or a combo off both that cap rate would stay the same.Now other metrics would change as a result of the structure used.For very nice single family areas many investors will accept 1% rent to purchase price.

The question is how do I structure the deal to make it work out for all parties?

Check that with your tax advisor and structure the debt between the properties from an income tax perspective accordingly.  

I have many physical issues.

Pay particular attention to how much of a deposit you need to provide, to be authorized to bid.Look into the fee structure they site charges and if it is above and beyond your bid price, or included.Download their "sample contract" and go over it...Then...

You can't always base your analysis at what the MLS data shows for rent but physically go look at it and see what you can do to increase rent to make the numbers look good.

You do need to consult with a local attorney and CPA to set up a structure that fits your plan.  

The cost to replace will depend on whether those are still structurally sound enough to sister in new joists ( basic labor job plus lumber ) or if they are crumbling and need to be removed to be replaced ( major job, skilled labor, temporary supports, remove and replace ).

Can anyone recommend a structural engineer in the Bay area in the commercial/industrial space?

We use to physically collect the rent every month.