I just bought a 2004 Coupe. I've driven it a few times in the rain with no problems. Yesterday in a torrential downpour it started skipping and stalling big time and check engine light came on. Any suggestions? Wires? Coils?

 

Have you tried using a scanner to see if it's giving any codes?
You can try pulling the engine cover off and checking the plug wires. See if they're loose, worn, or cracked. Also check the coils for cracks on the front and back of them. Just unbolt them one at a time and inspect them.
Your seal for the MAF sensor might not be on correctly and water might be getting into the throttle body. The seal is on top of the intake housing. Try putting a little silicon grease on the rubber seal to make it seal better.
Your best bet is a scanner though.

 

Engine light on? That means you have a code. Get a code scanner and come back with the code. You can buy Bluetooth ODBII interfaces to connect your phone to the car and then download an ODBII app.

 

did water leak into the passenger side footwell or trunk?

 

Translation: "My check engine light came on, which means the ECU (engine control computer or unit) sees a problem, and generated one or more codes to help me know what is wrong".
STOP right there, you are wasting your time and ours if you have codes and do not tell us what they are. Even the CHEAPEST ($30) ODBII readers will read the codes for you. IMO, EVERYONE should have a code reader and know how to plug it in and grad codes - with the codes, we can be of much more help.

That response, right out of the gate, is a good reason as to why I send people to Rob at Needwings so often.