Water in footwell and fresh air door/flap mystery. Please help!
 

After I found my rear footwell full of water, I removed the entire passenger seat and everything else in the passenger side (carpet, computers, etc.). I found and cleaned/degreased all drains (both sunroof drains, both drains under the windshield and I even pulled the fender liners and flushed the body drains). I've replaced the blower motor and regulator and I let the car dry out for a month, yet somehow I'm still getting water in the front passenger well and the only thing that sticks out to me is that the fresh air door/flap will not close. I know the box is draining and I've done all of the beginner stuff, but somehow water is still getting in and I'm out of ideas. I have no codes and there are no drivability issues. The A/C and heat blow fine and the drains are all 100% clean and clear. I'm completely stumped!

Can anyone help?

Thanks.