Nicole, perhaps if you provide a direct link to the help topic you are using and the version of the software, someone may be able to help. There is no 'multivariate analysis' in Pro, but lots of multivariate tools.
As for the last issue, the process apparently wants at least 2 'seed' locations and no more than the number of points in the dataset. It remains to be seen whether you have to select records within the point set or whether they have to be two or more points in a different featureclass.
As for the Projection question... a projection is when the data coordinates have been changed to planar coordinates from spherical coordinates. If your input dataset does not have a 'projection' (eg. UTM, Albers etc) then it hasn't been projected.
When repair geometry was done, you should now have no more invalid geometries, which is good... you just don't get a message to that affect.