For the past year or so, whenever there is a really heavy rain, my Expedition will run rough for about 2 hours, as if there is a misfire. I have close to 90k miles.

The SES light flashs at idle when it's misfiring, since the engine was idling at a low RPM, but there would never be a code... until now.

I got a P0300 (Random Misfire) and P0302 (Cyl 2 Misfire), and pending codes of P0171 (Lean) and P0303 (Cyl 3 Misfire).

I'm assuming water is getting into an ignition coil and is taking time to dry out. Would I be right in assuming to replace the coil and plug on cylinder 2 first? Or is there something else I should try first? And the Lean code is just due to the misfire?

Thanks

 

Just a thought, and I'm not as familar with the newer gen of Ford's '97 and up. I noticed when I was working on our 2000 Exp., the ECM is located on the passenger side and it looked like it is in an area that could allow water to run down or splash around the plug and the module. Wiring could be corroded or loose near the plug or the module itself. Other than that, perhaps the COP's(and that may not be the correct name for newer ignition systems) for 2 & 3 are stressed or cracked and the excess humidity or moisture is creating the misfire. I could see the Lean code and the misfire being related, especially if 2 cylinders are misfiring. Other than that, other thoughts are leaking intake gasket or exhaust leak close the O2 sensor.

Another thought, would be to run engine for a few mintues and then shut it off. Using a spray bottle for water, Mist the area around the ECM and plug. Start the truck again and see if the problem occurs. If not move on to Cylinder 2 and 3. See if the problem occurs again.

 

If it were me, I'd swap the coil pack and plug boot with another cylinder and see if it moves with the coil pack. Also while you are at it, pull the plug and take a look at it's condition, if they are worn, now is a good time to change them (and remember anti-seize is your best friend between the spark plugs and Ford aluminum heads).

It's probably either a bad coil pack or plug boot, but for the few minutes it takes to swap the coil packs, you'll sleep better knowing for sure, and you also may wind up saving some money by not swapping out perfectly good parts.

 

We had a similar issue with ours when it rained.
It started with an occasional misfire at idle and no codes.
It got progressively worse until we got a P0306 and P0307.
Cleared the codes and after it stopped raining it would eventually dry out and run smooth.
After pulling the COPs you could see moisture inside the boots and the springs were rusted.
The COPs were originals with 120k.
The firewall insulation pad was not installed straight and water would drip onto the #6 and #7 plugs.
I suspect water would collect around the plug, turn into steam and get into the boot.
Changed the COPs and the misfire was gone.
Trimmed the firewall pad, caulked the trim and no more water dripping.
I replaced all the COPs because of the mileage, but I kept all the coils.
I think I could have just got boots and springs.

 

The rough idle may be an indication the Idle Air Control valve is bad.
The IAC controls all air flow into the engine at idle with the throttle body closed.
I'm not sure, but I think the IAC is supposed to be closed after the throttle body opens up for higher RPM.
If the IAC is sticking open a bit it might be throwing off the air to fuel mixture.
There are no codes associated directly with the IAC.
What codes are you getting when the Check Engine light comes on?
You could try removing and cleaning the IAC to see if it improves anything, but once it starts corroding it probably won't last long.