- The ORIGINAL amount of the 1099-R is included in 1040 5a
- But because it is designated as non-taxable, it doesn't transfer to 5b
If the pension is designated as non-taxable on the 1099-R (box 1 is the gross amount and box 2 is zero), then line 5a on form 1040 should be the gross amount and line 5b is zero. Stop there. You don't make any further adjustments anywhere. (The linked instructions did not cover this situation, where the pension payer has correctly reported everything on the 1099R and no further adjustments are needed.)
If schedule C's Housing Allowance amount is left BLANK, then the amount doesn't translate into the program as a SE eligible.
I don't understand what you are doing here. Your pension should not be entered as a housing allowance on schedule C or schedule SE because it is not compensation for work you are performing. If you have an independent sig gig as a clergy person that you report on schedule C, and that position also has a designated housing allowance, it must be included as income subject to self-employment tax even if you are retired from your main position. It will be on line 2 of schedule SE, and that flows from lines 5a, b and c of a turbotax internal worksheet called "Schedule SE Adjustment Worksheet". But there is no way for your 1099-R pension income to "leak" onto schedule C or schedule SE unless you do something wrong.
