So I have water coming in from between the glass and the inside the molding where the clips holes are located. Where would the source be and does anyone else have this issue with 1st gen hardtops? It drips on to my trunk floor. So aggravating! Body shop told me the glass has to be removed. I'll post a photo when I have the car back.

 

The trunk floor of mine was wet as well a couple years back. That leak turned out to be the gasket around the 3rd brake light above the glass. Fixed it myself easily. That issue is more common with 1st gen hatchbacks than yours. Good luck.

 

+1 check the gasket on the rear center brake light. Then check the drain tubes ( disconnected or clogged) on the rear if you have the sunroof.

 

I didn't think about the sunroof drain tube, I had replaced the gasket on the center brake light last spring and still have the leaking.

 

+1 on checking those rear drain tubes.

 

I have a leak here too. When I found out what was going on my battery compartment.net was full of water. I drilled a drain hole. It didn't solve the problem but it doesn't rain much here in California.