OK I'm going to answer my own question as I figured it out, so this may be helpful to others:
-Copy the .mod file for the mission you want to play from the modules folder in the main game folder into my documents/neverwinter nights2/modules folder.
-Rename it by removing the preffix numbers, (so for example; 2400_Illfarn_ruins becomes just Illfarn_ruins).
Now it will show up as a new module for separate play. When you enter the module you'll first enconter a companion selection module, which makes me think this was an original intent of the developers but never implemented for the release.