1999 Toyota Corolla Car shuddering and CEL on?

This morning my wife was getting on the interstate and the car was running fine. She got to about 50/60mph and the car started to shudder/miss and the check engine light began to flash. She said upon applying the breaks it sounded like the car was going to "stall". It never completely died and we were able to pull it off to a parking lot and had to leave it due having to make it to work. We always run mid-grade gasoline in it. I changed the engine oil a week and a half ago and always keep tabs on it and it seems fine.

The check engine light flickers a few times and then stays solid but upon turning the car back on it is gone. I haven't had an opportunity to get the CEL right read but at the rate it is staying on and going off i'm not sure how well that will work.

The only thing we have done different this week is we left her car at work several evenings and rode home together. Now on three of these evenings we have had terrible rain storms. Is it possible that water got into the engine bay/spark plug area and are causing them to short out? I'm at a loss and don't want to dump a lot of money into a car that is 10 years old but I am not ready to purchase a new vehicle either (the ultimate catch 22)