Update:

Seems to be coming from the Driver's side. Tail light gasket, trunk vent, soft top drains have all been double and triple checked and are clean. It looks like it's leaking onto the floor of the trunk then dripping down into the trunk well.

 

Make sure your trunk gasket is still soft. I ended up adjusting trunk lock and it helped. Now I have to slam trunk with more gusto

 

Have you also checked the fuel filler neck gasket? Not sure it would leak inside but it is one more place that holds water at bay with a gasket/grommet.

 

Did you check the plastic bumper retainer that is right beneath the quarter panel. The corner of the bumper snaps into it. The plastic piece has three taps that go into the inside of the trunk.

Did you ever try taking out the interior pieces of the trunk and spraying the car down with water like I suggested earlier?

 

Sprayed the car down. Leak is coming from the soft top tray I believe. Pictures below:



This is where the water is dripping down from:


Same spot, from below looking up:

 

I am in a similar boat with my 08' with 150k. The trunk seal was replaced and top drains are not the source of my problem. For my car it appears to be a seam that's leaking. I'll try to take a picture later. If you open your trunk lid there is a gutter that runs around 3 sides of the trunk between the trunk seal and the sheet metal. In the back left corner of the gutter there is seam and when I ran water over this I found that inside the trunk it is wet underneath there on the ceiling of the trunk. It was wet on the left and not the right. So I put some silicon grease to confirm and my trunk doesn't fill with water anymore. I will eventually use silicon sealer there.

Maybe that's your problem too? Maybe yours is related to the hard top mounting holes?

 

Did you have pics of this leak?

 

I had a leak where the window plastic met with the vinyl

 

I just took pictures today of the area I'm describing from the outside of the car, have yet to upload them. I have had zero problems though since I silicon greased that area of the trunk rain gutters.

 

I think i had same exact leak. Had to take off small trim cover to fix leak. I used drip chek body sealer. 3m makes it. Flexible and paintable after drying.