Is there a way to add or take items out of the Favorite and Navigator boxes?
In the Favorites you can "Remove" an item by right-clicking (or Ctrl-clicking) on it and then choosing the "Remove" menu item.
The Navigator will always show all mounted volumes. Finder "Sidebar" items can be hidden. You can use the Navigator/Favorites preferences to remove the "Sidebar" items. Just right-click on an item in the Navigator and then uncheck the "Show Finder Sidebar items in Navigator" checkbox.
-Kirk