Oh, well it's not working because you had modified the Compact Menu System in order to add Quests in manually, but that is not necessary. The Quest System is designed to add itself to the menu.
So, get a clean copy of the Compact Menu System and replace the copy you have. Then paste the Quest Journal (with the above stated modifications) into your project and below the Compact Menu System, though still above Main.
Actually, you also probably want to change the line:
@command_window.x, @command_window.y, @command_window.z = x, y - 12, z
to:
@command_window.x, @command_window.y, @command_window.z = x, y - 24, z
You might want to do more to change the positioning of everything in that script really, since adding commands tends to throw the positioning off. You probably want the targetting window to be taller too.