How do I complete the set up of my "user" channel list? I put in the check marks for my favorites, but no channels were left off the list.

The list should save automatically.  Hit the Guide button twice and select Favorites.

I had problems with this, too.  I had to slow down and only add or remove the channels one-at-a-time.  Sometimes I could do 4 or 5 at a time.  Even then, there would be times when the channels would reappear after I had deleted them.  I have a Contour 1.