Turn off knock control temporarily and see if it goes away, and log timing sync errors to see if they are accumulating. having an error once in awhile (like 1 every minute or two) is normal. If that doesn't fix it (and you don't get lots of timing errors) it is not the harness. As long as you completely followed my software setup instructions, any fiddling from the multiplex setup was overwritten by the new dwell setup, and if it is firing on all cylinders the wiring is correct. I had an issue similar to what you are describing and narrowed it down to grounding issues.
Try grounding the EMS case to the grounding wires in the harness (just use a fork terminal under one of the screws) - that cleared up a lot of problems for me.