I just had an issue with my KS after a plenum pull. I pulled/broke the wire off the sensor in its original home in the nether regions of the motor because it was hooked to the plenum by a zip tie and I didn't realize it until it was too latee. It was in pretty rough shape though, very brittle. Anyway, when I dismantled the sub harness I was interested to see that there were two wires coming from the main engine harness, but that under the insulation, the black wire became just a wire "mesh" that surrounded the white wire. I think there is only one wire that actually attached to the knock sensor. In trying to figure out if this was right, I looked at the wiring diagram at
http://z32.wikispaces.com/ECU+Harness+Diagram, and it shows just one wire, the white one, and the black one is just some kind of shroud. So I think the sub harness you got is correct.
Have you tried resetting the ECU? Disconnect the battery overnight, and this should clear the codes, then you can start over and see if it still shows up.
Scott