HI Joe,
Brian is the expert and everything he has said matches my understanding.
Where is your SEP-IRA that you would be able to take a distribution without going through the custodian? If you have a "checkbook IRA," I hope you were told at the outset to get very familiar with the rules on managing it - one of the biggest is that you can't make a contribution or take a distribution without it going through the custodian for IRS reporting purposes.
How to take as a distribution a property owned by the IRA:
1. The custodian will require you to get a valuation of the property by a realtor or may require an appraisal by licensed appraiser. This is so they know the dollar value of the distribution. I'm actually going to switch custodians because my current one requires an appraisal and I'd prefer to just be able to get a BPO (Broker's Price Opinion).
2. I don't know how the property is currently titled. Mine are owned by an LLC whose only member is my IRA custodial account (a checkbook IRA). So the process for me has been that my IRA LLC deeds the property to the custodian and they deed it back to me personally. So there are two deeds that get recorded.
3. If your SEP IRA is not a Roth, yes the value of the property will be reported to the IRS as if it were a cash distribution and the full amount will be added to your taxable income. The properties I've done this with were free and clear. I'm not sure what the reporting calculation is if you've got a mortgage.
Hope this is helpful.