Okay. This is what I have gathered so far:
You have a single-extruder Bukobot, but are using an Azteeg X3 controller.
When you look for documentation or ask for help, don't think about X1 any more. You have X3. You can consider yourself the owner of a Bukobot Duo, but with one extruder missing (and perhaps with a narrower frame). You can continue to use the Printer Profile (in Slic3r) for the single-extruder Bukobot, because Slic3r doesn't distinguish between X1 and X3.
I am looking at this image: http://bukobot.com/_detail/wiki:jitsbuild:azteeg-mounted.png?id=jitsbuild-wires
In this image, along the right side of the board there are five small driver boards, plugged into the top of the Azteeg. If you peek under them, from the right, you should see three jumpers under each. If you instead see pairs of gold posts where jumpers could be installed, the jumpers need to be installed. Each pair of gold posts needs a jumper. (See the picture in the next post.)
The pair of thick wires from the extruder heater connects to the screw terminals labelled H-END1 (along the top edge).
The pair of thin wires from the extruder thermistor plugs into the two gold posts labelled E0 (along the left edge).
The bundle of four wires from the extruder stepper motor plugs into the connector next to the driver board labelled EXTR1 (along the right edge).
The motor connector probably needs to be flipped over relative to the way it was on the X1. If you don't remember which orientation you used before, it's easy to find out the correct way: Try it. If the motor turns the wrong way, flip the connector over.
To test the extruder motor, issue the M302 command through your host software and then tell the extruder to retract. (If you currently have filament in the extruder, keep the filament away from the Tatsu drive gear by shifting the lever.) If the Tatsu drive gear in the extruder rotates in the direction that would pull filament up and out of your extruder, then the connector is correct; if it turns the other way, flip the connector over.