It was removed because the dev (Pudding Hux) has been gone and (IIRC) has stoped updating the Yogbox.
Onto your very long post...
First, the darkness beckons is part of the minions mod. In the Yogbox it has been tweeked so that to activate the mod and summon minions, you need to find a special item in one of the dungeions. When you find that the M key will bring up a popup with more info.
Duncan is likely playing an older version of the Yogbox, you can "downgrade" your version by selecting "options" in the Launcher and then "Use manual build" then selecting an older version from there. (Try either the recommend build or the on just above that as Duncan is using minecraft version 1.2.3)
Finally, as I stated, the Yogbox developer has stopped updating/supporting the Yogbox. Thus the pack will never be updated (until PuddingHux comes back [doubtful]) thus the only was to "update" it is to manually install the newer versions of the mods yourself.