Again this is just documenting according to terms of the lease.This will be a trying time for landlords, but by documenting everything, and following the terms of your lease, you will have the proper documentation later if you need to go to court or if you need to talk to YOUR lender to ask for a loan modification.

What information should I be asking these businesses to provide to properly vet them?

We are not talking which milk to buy or pair of jeans. 

In San Diego proper (I grew up there, but don't invest there so don't know it as well) areas like City Heights will cashflow better.

Understanding how to properly outsource, how to deal with buyers (this was my first purchase, flip & listing).

Understanding how to properly outsource, how to deal with buyers (this was my first purchase, flip & listing).

Plumbing Check: Run water in all faucets ensure draining properly and no leaks.

I believe that any time is a good time to invest as long as the property checks out and cash flows properly.

I'm not opposed to setting up my books properly from now on, but am afraid it combined with the late filing will trigger an audit. 

It will still shield liability, if properly setup, and as long as your actions don't "pierce the corporate veil".