If the sellers disregard for the deadline makes it impossible to do the deal then move on. 

I’ll be the single General Partner for the deal and already have bought properties in another LLC (disregarded entity).  

Since the QOF must file IRS form 8996 I assume it must file its own tax returns, so a disregarded entity like a single member llc will not be good enough.

If it was a single member LLC it could be considered a “disregarded” entity without a tax return being required. 

If you're employed with a W2 Salary and are investing in rental properties under a LLC (disregarded entity), would you even be able to make deductions if they add up to be less than the standard deduction on your personal return, $24k in my case as I file a Married, joint return?

I am IRS will disregard the single member LLC for taxation.

That's what I see most often is like 1 Partnership that has a bunch of disregarded LLC's under it. 

If revocable living trust then no further tax implications at this time as will be disregarded for tax purposes.

It’s all about what’s the easiest way to handle the property for TAX reasons, a single member LLC is a disregarded entity so it’s just you with a fancy name and a limited liability to what’s in the LLC.  

When your 2019 taxes are in & processed by the IRS, your income calculation will be based on either 2019/2018 average, or just 2019, but either way 2017 will be completely disregarded as a data point.No reason to bark up the HML or non-qm trees when you can just wait a month or two, the benefits of the "Great Deal" you are looking at in terms of getting 7% off fair market value, or another $150/mo in cashflow from that, will be FAR outweighed by the rate/points/fees/etc that come with a HML or non-qm.