I never filed for reciprocity at my Minnesota job, so now I need to figure out how to get the MN taxes back that I paid. I looked on the IRS website, and it looks like I need form M1. One section told me to fill out M1-NW (Non-Resident) and another told me to fill out a different form instead.
Has anyone done this? I am very confused about which forms to fill out.

If you did not file for reciprocity, you will actually have to PAY the Minnesota taxes, then get a credit for paying those taxes against the Wisconsin tax return.