I think you need to understand the difference between wages designated as housing allowance and pension designated as housing allowance. A pension is never subject to self-employment tax or social security tax, even if you are a retired minister, because a pension is not compensation for services performed.
I’m not going to read the entire 120 page PDF, I have read similar ones and I have been working in this area for several years. If you want to point to a specific page that is the source of your confusion, I will review it, and see if I can explain further.
Because your 1099-R correctly reports your pension as non-taxable in box 1 and 2a, you simply enter the 1099R on your tax return, and make no further adjustments. Report any other income in the usual way, either schedule C or on a W-2. If you are referring to the Deason rule, which requires a calculation to be performed to determine the percentage of business expenses that you can deduct based on your taxable income and housing allowance, this does not apply to your current situation either, because, as I said, even though the pension is designated as a housing allowance, it is not part of your compensation for services performed.
