Can I file taxes with a ministry housing allowance for 6 months and regular income by the same organization for 6 months? (1x w-2, that includes SE income)

Yes, you can normally file taxes with a ministry housing allowance for 6 months and regular income for 6 months from the same organization. Your W-2 will normally include both types of income. The housing allowance should be excluded from gross income for income tax purposes but is included for self-employment tax purposes

For more details, you can check out these resources:

• IRS Topic No. 417 - Earnings for Clergy