2001 Ford Escape runs rough when it rains

The Check Engine light is telling you there's a diagnostic fault code stored in the Engine Computer, and it's related to something that could adversely affect emissions. The place to start is by having the codes read and recorded. The people at many auto parts stores will do that for you for free. Reply back with those code numbers, not their generic description.

The ignition system is the logical choice since that is the only system that is adversely affected by water. Regardless, the fault code most likely referred to which cylinder was responsible for the misfire. A wet ignition coil is a mechanical problem with an electrical circuit, if that makes sense. An electrical problem, like a loose or corroded connector terminal, for example, would be detected by the Engine Computer, then the fault code would specifically make reference to that type of failure.

Any time you hear a diagnosis starting with, "could be", it's a pretty good bet the code just indicated which cylinder was responsible. Fault codes are just the starting point in the long list of diagnostic steps. Understand that fault codes never say to replace parts or that they're bad. They only indicate the circuit or system that needs further diagnosis, or the unacceptable operating condition. If an ignition coil is the cause, you should be able to see or hear the spark snapping while the engine is running and the problem is occurring.