I need assistance with a complicated payroll situation

One time job. I'm transitioning a pastor from being a w2 employee to self-employed contractor and I need to know how to handle this. We did not withhold enough last year and now I am getting 941 notices for us to pay his taxes from last year to cover the underwithheld withholdings. But now, should I modify his w2? I just need help but do not have time to go on hold with IRS for hours to get this sorted.