If you just want to remove menu items from this theme, you can also just unset() it inside the template_menu() function. I don't know the variable names off the top of my head, but it would look something like this.
unset($context['menu_buttons']['help']);
That would remove the help button from the array. Put it right before the foreach() loop in the template_menu() function. You can unset as many as you like.
unset($var1, $var2, $var3);