The IRS prohibits certain transactions between the IRA and its owner (or certain related parties).

Ensure you understand and comply with all IRS rules regarding prohibited transactions.UBTI (Unrelated Business Taxable Income): If you use a mortgage or financing within your IRA to purchase real estate, you may be subject to UBTI tax if the property generates rental income.

I have a clause in the lease that prohibits this. 

Given that a prohibited transaction will result in the IRA account that engaged in the transaction being considered fully distributed, I don't think you want to be in a gray area.I guess you might do a partnership with your IRA.

I know 2 years ago when I was doing mine that was strictly prohibited.

I've reviewed a number of such codes and they almost always prohibit bandit signs. 

You may not step in with personal funds to cover expenses of the IRA as that would create a prohibited transaction.Your only means for adding capital is via new contributions to the IRA, which are limited.

Some jurisdictions prohibit or restrict this in their zoning....BUT if you can get around all of that, I think the upstairs apartments might be perfect for AirB&B...You would not have neighbors complaining about people coming going, different neighbors every week...and on and on.  

Under limited and very narrowly defined circumstances disqualified persons to an IRA may partner with such IRA.In the scenario that you present, in which the property will be held by an existing LLC of which you're the member, using funds from your IRA for a down-payment would certainly be a prohibited transaction.An alternative would be obtain a private loan from an IRA of a non-disqualified person to fund the down-payment.

Good to know that a carriage house might be better if other STRs will be prohibited with the new laws.