Did you even have a intake bypass valve? Its suppose to trap the water from getting to your motor. It doesn't always work the way it should. I mean you can't go over deep water and into a large puddle. Its more for daily driven in the rain. Is your CAI 1 piece or 2 piece... if its 1 piece then you don't have a intake bypass valve. If its 2 piece you would have a filter/sponge inbetween the 2 pieces of pipe. My CAI is 2 piece and is lacking the intake bypass valve. I'm going to getting one as soon as I find one locally if not I'm ordering one. This storm that just passed us I took the lower pipe off the put my filter in the upper pipe to make it a short ram. Good way to stay away from this hydrolock mess. Did the car shut off immediately after the puddle or did it choke up? You might want to drain the oil as well and then pour oil to flush out any excess water. Since you found water in your number #4 cylinder its more likely hydro lock. But with cleaning out the water from the engine there still might be a chance that the engine will run again.