If 100% of your comp is housing allowance, then the church does not need to send anything to the IRS, either W-2/W-3, form 941 or 944, or 1099-MISC (unless they have other employees, of course).
If you have a second self-employed business then you need two schedule C's, one for each. You can deduct expenses for business #2 on schedule C #2 as usual. You just can't deduct pastor expenses on your pastor schedule C. (In fact, I'm not even sure if you will have a schedule C if you don't have additional cash income to report, you may just have a schedule SE.)
And of course, even though the housing allowance is excluded from income tax it is still subject to SE tax, so your schedule SE should include both the housing allowance and the net profit from business #2.
