Oh...I think you are plugging in the wrong harness to the cdi. The colored wires you are mentioning here are the main electrical wiring. You have no need for the plug you are connecting to the cdi. This is an error I have seen before.
Ok...I had the same problem with that extra 5 wires coming from the engine. I read somewhere that these wires are for shifting indications only. Its seems that in other countries every gear is indicated on a speedometer or something. In other words, they are of no concern unless you have...