@Adam Soyak and Account Closed is your guy.Or use the modern technology and work with any of the tax accountants on this forum remotely.

I grew up in the area (Maryland) and attended school in state before moving up to NYC and then SF for work in professional services (consulting, strategy) and technology.

Even if I agree with your premise that having a non-rounded purchase price makes the loan process more difficult (I don't cede this point at all btw because you have not provided any objective proof of its impacts) It is a minor problem at best, that any professional should be able to over come.

I'm having difficulty finding insurance for this arrangement. 

The problem is difficulty in matching houses sold to the house I am working with (there's actually 3 houses in the same 1 mile radius).

The difficulty ins sub metering is that I don't believe that my plumbing is split by unit.

As many mentioned here, you will have difficulty coming back to the Bay Area market if your sold your only property. 

There are a lot of scary similarities in the market right now as in 05, 06, but agree that the shortage of affordable housing (builders are just now starting to build them, way after the fact) and labor shortage (kids uninterested in the trades) will delay the arrival of a correction (agree it will come eventually).Plus the employment base in Phoenix is much more diverse now than 10-15 years ago (construction & financial) to a lot of technology and corporate support services recently added. 

There is a lot of technology available to help you manage your properties.

Thankfully with the technology of today; there is a huge opportunity to wholesale from a distance that if you two can master it...you can acquire property anywhere.