The Shadow Crypt/Instance Paths

Overview
Each instance has 14 rooms: a entrance room, 12 regular rooms with gear and finally a lever room. Rooms have a color and a type. For each color, two out of five types are always out of play. Thus, 4 colors * 3 types = 12 rooms.

Definition of Types
You cannot tell this by map due to overlapping floors (although can possibly know where you are by height from /loc command). There are various ways to name these rooms.
 * Attic, or Columns, or Pillars
 * The room with the stone pillars and a central chest.
 * You fight Umbral Gargoyles
 * Maze, or Gate, or Jail
 * The maze-like room with the lattice-walls. chest is placed randomly in four coners.
 * You fight Spectres and Shadows
 * Pyramid, or Alter, or Deis
 * The room with the stairs ascending to a central chest.
 * You fight Phase Spiders
 * Torch, or Fountain, or Puzzle
 * The room with the four torches, each torch has fountain on its back wall, and the fountain indicates correct order to light torches in binary format.
 * You fight Shadows and Umbral Wolves
 * Water, or Underwater
 * The room you have to go through underwater maze.
 * No enemies in these rooms

Instance Variations
There are three different versions for a instance of this dungeon.

In order to figure out which version you are in, after you've cleared the first emtramce room and picked up the Death's Door clicky (2 charges Dimension Door), go east.
 * If you are in a  blue  room, you are in what will be referred to as Instance 1.
 * Otherwise, you will either be in a  green  room - Instance 2
 * Or a  red  room - Instance 3

12 Gears Walkthrough
If you want to be walked through the dungeon using the shortest possible route, collecting all 12 gears along the way and enabling you to open the extra chest at the end, then follow this guide, otherwise refer to the Maze directions in the next section.
 * Go east and get to a  blue  room - Instance 1
 * Dimension Door to the beginning
 * from the start:
 * North to green underwater
 * West to blue maze
 * West to blue torch (lighting order: south, east, north)
 * West to blue underwater
 * West to red pyramid
 * North to yellow underwater
 * North to yellow attic
 * North to yellow maze
 * South to start. Shrine now if necessary - you won't be coming back to this room again.
 * South to red torch (lighting order: east, north, west)
 * North to green pyramid
 * West to red torch (yes you have already been here)
 * West to red attic
 * East to green torch (lighting order: north, south, west)
 * East to end game


 * Go east and get to  green  attic - Instance 2
 * East to green maze (if you can't get to the gear from here, just proceed to next room)
 * East to red maze
 * East to yellow pyramid
 * North to blue maze
 * North to red underwater
 * North to red torch (lighting order: east, north, west)
 * North to green torch (lighting order: north, south, west)
 * North to blue pyramid
 * North to blue attic
 * North to green maze (you should be able to get the gear from this direction now if you couldn't before)
 * Dimension Door to start
 * West to blue attic (yes you have already been here)
 * South to yellow torch (lighting order: north, west, south)
 * West to start. Shrine now if necessary - you won't be coming back to this room again.
 * South to red torch (yes you have already been here)
 * East to yellow underwater
 * West to end game


 * Go east and get to  red  attic - Instance 3
 * East to blue maze
 * East to red pyramid
 * East to red underwater
 * East to yellow torch (lighting order: north, west, south)
 * South to blue underwater
 * South to green attic
 * North to green maze (if you can't get to the gear from here, just proceed to next room)
 * West to green pyramid
 * North to green maze (you should be able to get the gear from this direction now if you couldn't before)
 * Dimension Door to start. Shrine now if necessary - you won't be coming back to this room again.
 * South to yellow maze
 * East to yellow pyramid
 * South to blue attic
 * South to red pyramid
 * West to end game

Maze
Taken from http://www.themacguild.com/forums/showthread.php?t=533



You can also figure out which version you are in by using the map. Once you make your first jump, take note of which color and type of room you are in. If you go to the West for your first door/teleporter, you will end up in 1 of 3 places:
 * Green Columns room, West doorway [GCW]
 * Blue Columns room, West doorway [BCW]
 * Yellow Underwater room, West doorway [YUW]