With that amount of water, you can do some testing to find the exact spot.

For the sunroof, open the roof, and pour water (I just used a water bottle) down the side channels. Obviously, pour somewhat slowly so the water doesn't overflow into the car! If these are working correctly, you'll very clearly see a stream of water pouring out underneath the car (below where the A-pillars end).

Do the same thing at the four corners of the windshield. And maybe at the points where the roof rails attach to the car.

I wouldn't suspect the door seals (or side windows) per your description. I've found these just end with damp carpeting. But these can be tested by spraying down the sides of the car with a garden hose at full blast.

__________________
Rusty, Beater 2001 X5 5spd

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2017 VW GTI
2001 E46 Wagon (manual of course!)
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