breif history: Well first of all, I replaced my water pump, as well as, my timing belts. After the job was complete, engine did not run right (kind of retarded). I had to do a few things to the distributor and that helped a little bit. I redid my timing again and I notice that the front balance shaft was off about three tooth. As for the rear balance shaft, when the shaft is locked in from behind the engine, the timing marks on that gear did not align with the mark on the engine. I reset the front bal shaft but on the rear, when the shaft is locked in behind the engine, the mark goes off and doesn't align with engine mark. So did the best I could to align the marks. However, the shaft did want to lock in. The result were a little better but not good enough.

Q: Would the balance shaft have the capability to throw off the my engine performance ( engine's retardedness )?