Here is another thread with the specific molex connector numbers, and pay attention to Dr. Joe's instructions in that thread.
For wire we used 3-conductor shielded wire; since the signal voltage is so low in the PWM inputs/outputs it is very sensitive to noise from motors and using a shielded cable rather than the IFI PWM cables can make a huge difference for things like yaw rate sensors or accelerometers. It's a little stiffer too and less likely to flop its way into unwanted areas like gearboxes.