My 2003 5.4L with Coil on Plug ignition got wet, now it runs rough. OBD says misfire cyl 1 and cyl 2. I thought it would dry out in a few days but it hasn't. I assume the coils got water in them and are bad. Is this normal?

 

Yes, these motors like going through COPs. If it still running rough try checking to see if there is water still down in the spark plug well. Also pull off the COP and make sure the boot is dry. Other than that,you will have to replace the COP.

 

You're going to have to pull the COPs and plugs for those two cylinders at minimum. You might want to take this opportunity to change all of the plugs. Be sure to use a compressed air nozzle to blow out debris and moisture from the plug well before the plug is removed.

Check the plugs for cracks in the elctrode, and the COP body for cracks too. Check the plug boots for tears. Replace as needed. Put it all back together with some dielectric grease inside the COP boot before putting them back on the plugs. Good luck!