In my case the cheap coils were the source if the rough idle and car running poorly. My car has gone through two sets of cheap coils, one from Ebay (installed by previous owner) and one from Eurospare. The car run like crap with Ebay coils. With Eurpospares the car ran fine for a month, than started running like crap. I replaced the coils with proper coils made in Japan by Diamond. If you have the luxury, swap the known good coils from another car and see if the problem goes away. if it does - you found the problem.

What RPMs does the car idle at? Does the RPM change when you shift from park or neutral into Reverse or Drive? Does the car stall at low RPM, for example at stop signs? If it does, does the dashboard light up like a christmas tree when the car stalls? Does the car hesitate or stumble if you try to floor it on the freeway?

You can't trust the ECU to throw a misfire code in these cars. These engines have a 2-wire ignition coils, so the engine detects that "some spark happened somewhere in the circuit". So, if the spark happens between the cracked body of the coil and the cylinder head the ECU would be perfectly happy and no misfire codes would be thrown.

Other sources of idle issues could be Idle Air Control Valve (very cheap part), EGR problems, throttle position sensor. Water is known to get into the ECM plug where it connects to the wiring harness. Make sure that it's not corroded.