FYI, the holes in the sunroof are fully fictional and do not leak into the housing where the amp is located. We've had a lot of rain lately and the housing where the amp is located is swamped with water. =[ Had to take it to a professional to trouble shoot.

 

Try removing more carpet around the problem area. You might be able to spot where water is coming from. Is the trunk seal in a good condition?

 

I assume you mean functional and your browser decided to help... like my phone does =P