If there's hard rain and puddles of water, don't drive the car with a CAI. Hydrolocking an engine is a bitch. Get a By-pass valve. Like it was said before, it takes a lot of water to turn the oil milky, so check that out.

I would do an oil change quick, run it and see what happens. If it turns milky again there's something wrong. The spark plug test is also good to see why it is misfiring.

Oh yeah and get a bypass valve