on rainey days engine misses badly- engine lite comes on - dry days runs good

I had a similar problem on my 03' w/ 3.0. When I removed the Coil Over Plugs (COPS) there was water or evidence of water down in the head where the spark plugs are located. I dried out the plug wells, replaced the plugs and reinstalled the existing COPS using dielectric grease in the COP boot to seal out moisture. The grease had either washed away or been nonexistant to begin with. This cured the misfire, I unplugged the battery for 15 minutes to reset the engine light, I have not had a noticable misfire or engine light on since. When the COPS cause a misfire due to moisture infiltration and it is severe enough the check engine light flashes. The flashing indicates you need to service ASAP since your dumping unburned gas into the exhaust. This will burn up the egr and possibly melt the insides of the catalytic converters front and rear. When they melt and plug you will have drivability issues also. I am no mechanic but if your going to replace the rear COPS you should replace the upper intake manifold plenum gaskets since it needs to be removed for access.