In the wiring prep..... http://wiki.e3d-online.com/wiki/Big..._By_Step_Assembly_Process#Prepping_The_Wiring It says "Find the two Motor Cables, one will be longer that the other." Maybe you have followed the previous instruction to move the X-Carriage wires to the right, but with the wiring hidden it may be difficult to see which wires come from what braid. The "longer" motor wiring is probably obvious as it is the only one with a "black and yellow" wire with it, but as far as "shorter" there is a choice of three motor wires, two of the three coming from the extruder motors. If the origin of the wires may not be obvious from the way they emerge from under the base. Would it not have been simpler to code each of the four groups of wires (with a different coloured cable clip?) that emerge from under the floor to indicate where they come from?
Maybe it's too late for you now, but I marked all my connectors with a white permanent marker. Makes life a whole lot easier.
Ok I built a dual and the intructions seem a bit different. I followed them by word and didn't have any cabling problems even without marking. Did cabling, turned on, worked. But that is a reason why I read a manual of complex products one or more times before actually doing something to plan things ahead that might make problems...
Updated the guide to say the short one should have the Y end-stop in the same cable braid to make it clearer.