In order to invest in real estate with your retirement account you need a self-directed IRA or self-directed 401k. 

Still thinking of other options such as cashing out my ira if needed.

As for funding, I would look into a Self-Directed IRA or eventually making an S-Corp.

Will Charles Schwab or some other firm allow you to use a brokerage and or ira account as collateral for a re loan?

In addition to that, you can always pole family and friends to see if they have any savings or money in a self-directed IRA that they are willing to invest for a particular percentage fee once you refinance.

We also have greatly reduced our IRA funds because we are spending them on apartment downpayments.

I don't like the traditional 529 because those funds must be used for college expenses otherwise you incur a penalty.I read about setting aside a Roth IRA for them.

I ended up buying two cacao farm parcels in a newly created self-directed ROTH IRA – another concept that I wasn’t really familiar with until recently.  

Can I use a Self Directed IRA to pay off a rental property I already own?

IRA and saving account is big help in calculating your income.