It looks to me like the CD isn't even hooked up to the motor. All the wireing looks to be going up to the throttle/killswitch area. There should be 3 wires coming out the front of the motor, a white, a blue and a black. The blue wires from the CD and motor go together as do the black ones, the white wire you cap off or use with a headlight. The killswitch wires go to the blue/black wires from the CD, one to each side.
Hope I'm right about this, from the 1 photo I'm pretty sure
At least give me a look at the other side of the bike
Is the frame drilled with the wireing going in and out?