There are several routes the water can come in, and I think it can get in through the scuttle area as well. I'd personally check that it's not coming in through either the A-pillar location, or through the bottom of the door car. I know you have the hard top on, but if the seal is not perfectly aligned on that you can still get water coming through.
Might be worth sitting in the car and getting someone to spray a hose at you while you look for drips.