Ram Air IV

During the winter i have made a new PCM harness to my LQ9. I made a copy of the old one minus some cables that I did not use on the old harness. Every thing works except that missfires occures. I loosing the spark on one or several cylinders. It is less missfire when the engine is cold and a lot of missfire during acceleration(warm engine). The engine act normal before I changed the harness. The only thing that I have changed on the engine except for the harness is the spark plugs (Bosch BCH-4005), gap 0.60".
Magnus