Assembling the extruder:
Make sure all the holes in the extruder body are clear by using appropriately sized drill bits to clear any bridging layers in the print.
Insert a 6-32 nut into the trap as shown in the left of the idler here:
Insert the other two 608 bearings into the extruder body, put the idler onto the body and secure with a 1" 6-32 screw as shown below. DO NOT tighten the screw too much, it just needs to be snug.
Now get the hobbed bolt. Put one washer on the bolt and insert from the right. Note the position of the hobbing - it needs to line up with the hole just below it where the filament goes down to the hotend. If it does not, remove the bolt and add washers until it lines up. You may need to look through your washers to find ones of slightly different thicknesses to get the alignment close. When you're done, put two washers on the other side, put the gear on it and fasten the whole thing together with a nylock nut. Tighten slightly then back it off just enough that the gear and bolt spin freely without being loose.
Put a small 6-32 nut into the nut trap in the small gear as shown. This photo shows a regular screw in this photo but that won't work - use a 3/8" setscrew.
Now put the small gear onto the stepper motor - it needs to be completely flush with the body of the motor with the setscrew side towards the motor. Line up the setscrew with the flat of the shaft and tighten it just slightly for now.
Mount the motor onto the body of the extruder using three M3x10mm screws. Before you tighten it up too much, check to see if the gears line up properly. The herringbone gears need to be aligned. Loosen the setscrew so the small gear can slide around. Tighten the motor mount screws. The motor should be positioned so that the gears move freely but without undue backlash (looseness between the gears). When the gears are aligned with the motor tight, tighten the setscrew on the small gear.
Finally, mount the extruder to the X axis using two 6-32 x 3" screws. If your parts kit came with an extruder spacer, put that between the extruder and the X axis. You'll have to use the tiny 6-32 nuts on the back.
We won't be putting the hotend on quite yet.