I don't know how to add commands, but the environment variable has to be set in microsoft windows.
It depends on Windows version, you can find some help here: http://www.computerhope.com/issues/ch000549.htm
I can't open your file but I personnaly often use split surface and generate compatible mesh without convergence issue (what kind of convergence problem do you encounter ?)
I don't like to use the component-component as it creates contacts automatically and I like to know exactly what I am creating.
The separation distance and angle are used by Mechanica to choose whether it will create a contact between a set of surfaces or not.
As an example, if you set separation distance to 0.5mm, it will create contact between all surfaces separated by a distance less than 0.5mm.