I am having the same problem, but only misfires when the defrost or the air conditioner is on. The compressor for the AC cycles when you use the defrost heat setting, it doesn't run constantly, but without doubt sitting at a red light, I feel the misfiring, turn the heater OFF, and the missing goes away. I changed spark plugs and wires, it went away for a while just to return within 2,000 miles. My guess is that it is AC compressor, the spark plug wires, or the throttle position sensor out of range and not working. I will post what I find... If I ever figure it out.
I have changed the rubber elbows for the PCV tubing front and back side. I use the 90 degree elbow from a couple of spark plug wires I had around. It is a pretty nice fit too, with a little thicker rubber elbow boot that will stand up to the heat. The truth is still out there. I still have that miss at a stop sign or read light. This is like the paranormal, phantom symptoms that come and go.
When your A/C is on, you are loading the engine which will expose any weakness including a developing misfire problem, or possibly your A/C clutch or compressor is wearing out and seizing up. It may do this intermittently, but eventually it will fail. Turn on your A/C and watch the compressor, it should turn smoothly, if not, your compressor may be going out or icing up.
This is a common problem on vehicles with what we call Direct Ignition System. On this particular vehicle each cylinder has a coil install directly on the spark plug. When on coil fails, the check engine light flashed for this particular condition because raw fuel is getting into the exhaust system. This vehicle has atleast two catylic convertors. Raw fuel in the system will cause the convertors to overheat and melt down internally causing more expensive problems. The flashing light is telling your that the vehicle is not safe to drive. Have is checked by a professional ASAP. Be aware this is a fire hazard.