Wow! I have almost the same problem. 2001 Civic EX. My Fuel pump died. Had it replaced, now the car is really rough at idle after it warms up. CEL came on and the codes indicate misfire on all 4 cylinders. I reset the ECM/ECU whatever and it actually got a little better. Put in a new air filter and the problem came back. I'm not sure if that was just a coincidence or not, so I'm going to reset the ECU again.
I'm not sure what to test next.
Monday, September 19th, 2011 AT 5:26 PM