It could be the sunroof roof drains, too. Open your sunroof, and locate the drains. Take a cup of water and pour it in and see if it is draining out properly. Make sure your car is really nice and dry before you start this process.
Incidentally, I would recommend pulling your carpet out of the car if it really got soaked. The sound deadening material will certainly mold/mildew and the car WILL smell. Get the carpet out and get it really dry, let it sit in the sun if you can (I know it is winter) and don't put the carpet back until you find the leak. Windshield is possible, as is a weatherstrip sealing issue.
If the roof drains are clear, I would sit in the car and have a friend put water on it with a hose. Try and see where it leaks.