Drain Tubes
One other thing to check, while you're at it, is the drain tubes on each corner of the moonroof pan. If these are partially blocked, water can easily overwhelm the pan, and leak inside. With the moon roof open, direct a small amount of water from a hose or bottle into the pan, and see how it drains out. You should get 4 puddles of water under the car if everything is draining okay (assuming the car is on a level surface). If any are plugged, you can use low pressure air, or a piece of wire to clear out the debris. The moonroof "seal" isn't really a seal at all, but is only designed to slow down the water intrusion. It's the drain system that actually keep the water out of your car.
JD