Thank you for providing all of the information necessary to troubleshoot this issue. It looks like your
geo_em.d01.nc file specifies the pole latitude of your domain as the North Pole (90, 0). Because of this, the WRF-Hydro GIS Pre-processing tools were expecting this to be a North Pole Stereographic coordinate system. I made a change to the code and pushed the changes to the repository on GitHub, which will correctly interpret this coordinate system definition and properly place the domain over the McMurdo Dry Valleys. You can pull the current master repository and test this update for your domain. You asked about how to tell if the shapefile is in the correct location; this can be hard to do with just a domain boundary. I also like to use the "Export Grid from GEOGRID File" tool to export the "HGT_M" (elevation in meters ASL) layer from your geogrid file to check that topographic features are correctly georeferenced. See the attached screenshot for an example of what this domain should look like on your basemap. Let me know if you have any trouble.