2006 Honda Civic

On a 2006 honda Civic, I change the connecting rod bearing for cylinder number four. Now, there is a knocking sound when you accelerate, and when you are slowing down. I dont notice it at cruising speeds, although, I just may not hear it. I think sometimes, it can be hard at an idle. It wont make the sound when the engine is cold, but then after five minutes you can hear it. At idle, and startup, sometimes the car want to die. And after driving for about thirty minutes, the check engine light flashes. Now it is on steady. Ive changed the spark plugs, but it didnt make any diference. What could be wrong?