The drain hoses, by design, are very easily pinched by the headliner. Don't assume they will work just because you cleaned them. They will return to the pinched shape because they have been that way for a long time! Test them with a 32oz cup of water. Pour some on a corner of the roof. If the water doesn't come out the rocker drains, and goes inside, that's your problem. Try each corner.
The sunroof ALWAYS lets some water past, almost every sunroof does. That is why the drains are there. If the water comes out the rocker drains and nothing gets inside when you test this, you have another problem.
Check that the relationship of the panel to the roof is right, too. If the roof is not ending up in the right location when it is closed, it could let in too much water for the drains to handle. Rusty sunroof cables can cause the panel to not go all the way back to closed.
Additionally you can pour water pretty much right on the drains by gently popping the side black trim bits off the inside of the sliding panel (in closed position), undoing the four nuts that hold the glass panel to the frame, and carefully removing the glass panel. Lift it up, turn it, and bring it down into the interior, don't try to get it off over the top of the roof, you'll just scratch something. That way, you can stand on your front seat, stand up through the sunroof, and see exactly what is happening. If one corner is not draining, you'll see it immediately
The cables on mine turned out to be badly rusted. Since I had other things to spend $400 worth of parts on, I cleaned the drains, jammed the roof panel into closed position, and pulled the power for the motor. Haven't missed it.