Hello there, @bobbieK.
You can definitely correct a pastor's paycheck by adjusting its payroll liabilities. And I'd be glad to assist you with this.
Since the payroll tax liability has been paid. Let's use a liability adjustment to correct an employee's information. Please follow these steps below:
You can read this article for the detailed steps and information: Adjust Payroll Liabilities.
Regarding your 941 forms, you can manually calculate the taxes to correct it. And yes, the 941 shows different amounts for SS wages and Medicare wages.
However, I still encourage seeking assistance from your accountant so they can offer some advice regarding this matter.
Fill me in if you have any other questions managing your payroll. I'll be around if you need any help.