Why not just chose between the dragon or the Nameless to be the bad guy and play in a 4 grid board to be chosen at random (with some exceptions of tiles that need to be in play)? Any counter that should go in a space not in the game is simple ignored.
Do you think this may work?
Careful consideration needs to be given as to which boards are left out. A tile with a task may be revealed, but may not be fulfilled because the destination board is not present. Plus, almost every board has an important tile or two which can be pulled from the bag. Losing these encounters may take something away from the game. I meant to sit down and figure out which boards could be removed with only losing minimal tasks, but haven't gotten around to it.
What is your reason for limiting the game to a 4x4 board setup? There are variants on this game page which can cut game length and balance the weaker characters.