Also, I'm not sure if the dealer and the lender must be arms-length by the rules.Finally, on your side, the interest payments from the dealer to you are taxable income.

I cashed out my taxable accounts before the crap hit the fan.

is there a way to take some of the $ out of my ira & use it to pay cash for an apartment building without causing a taxable event?

Active on the taxable side of the fence. 

After all my deductions I am left with a small amount of taxable income and certainly not enough to justify paying a larger down payment and extra expenses.

First, if the property was acquired inside a Self-Directed IRA the taxable gain would already be tax-deferred (Traditional IRA) or tax-free (Roth IRA). 

For the personal property aspect of your purchase, you would have the option of accelerating the depreciation using Section 179 if you chose to do so, which would allow you to expense up to the entire cost of the asset in one shot to the extent that you have taxable income (it can not cause a loss, where normal depreciation can). 

If you are doing Estate Planning or expect to be in a taxable estate at some point, then you would need to get with a professional to determine what is the best way to take title for your specific situation.

There is no distinction between some of the $ that is pretax and some that is after tax.2: If you leave your job or get fired, you have 60 days to pay it all back otherwise IRS views it as a taxable event as slaps you with ordinary income tax on all of it plus a 10% penalty for early withdrawal.

You can do either scenario but scenario 1 results in a taxable event.