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Ok here is a weird one. My 99 Expedition was running great. I lifted the hood and sprayed off the engine (it was running) to get all the dust and dirt off of it. It started stumbling and I stoped spraying and shut the vehicle off. It acted like it was misfiring for about 5 days after that, and then today the check engine light went off and it is running fine again. part two of my dilema. I pluged a scanner in to see what the code was for the check engine light and it doesn't work. The scanner was checked on another vehicle right after that and it worked fine.
If you got water down in the plug wells, you could cause a miss or misfire. I would remove the boots and check them for cracks. Replace them if they're the originals. Take your expy to a parts store to see if they can read it. If they can, then check your set up on your scanner.
If the CEL was off when you scanned it, the scan tool won't get any codes (although a good scanner can see 'pending' codes if they are present.)
(After "n" key cycles with out the ECM finding the misfire the ECM will clear the misfire DTC and turn the CEL off (if that was the only DTC present.)
I guess it depends on what type of scanner was used. Mine has the ability to display pending codes. If no codes have been set, the display reads "No Codes" (duh). Thats why I suggested he take it to a place that will scan for free. If their scanner connects, then there isn't a problem with the interface. The problem may be with his scanner.