"then took that same amount out of my paycheck in those two months marked as federal tax withholding"
That seems to indicate that amount of extra pay/taxes have been added to box 2 (and box 1 if it was done correctly) of your W-2, so it has already been taken care of. You don't need to do anything else with that, as entering Box 2 of your W-2 takes care of it.
It sounds like you have not elected out of the Social Security system, I think #3 is the correct choice. However, I'll flag the clergy expert to verify that.
@Opus 17 No, don't enter the health insurance premiums as part of Schedule C (unless you ALSO have other earnings, outside of the W-2 income). You are an Employee for purposes of Income taxes, but Self Employed for purposes Social Security and Medicare taxes. The Self Employed Health Insurance deduction only applies to Income taxes, so you can't use that. You can still enter it as a Medical Expense for Itemizing your deductions, but due to severe limitations, that probably won't reduce your taxes.
