I found the solution.
I was missing the bolts under the gt window inside trim.
Credit to JamesBond007.
"Your better off trying to fix the hole from the inside.Most water enters the trunk through the wing stands, and it's a big job to remove the rear.
Rear Clip Removal
When trying to remove my rear fastback clip I really couldn't find many resources on how to do it so I decided to write down all the steps I an think of. Feel free to add to this if you have any info.
1. Remove Taillights
2. Pop the clips that hold the taillight harness and bulbs to the clip. (they're back on each cubby of the taillight portion of the clip. Also unscrew every nut and bolt that you can see back there. the only thing left should be one rivet on each side that holds the clip pieces together.
3. Remove rear 1/4 panels if you have not done so already (probubly optional in your case)
4. Not sure whether rear bumper must be removed, but mine was.
5. pop out all the plastic fasteners in rear wheel wells that look like they might be attached. I think there's 3 on each side that are actually attached.
6. Unscrew all the screws and nuts from the gas housing. (4 nuts and 2 screws or so)
7. take off all the bolts and clips on the black plastic piece that runs along the side of trunk and around inside of 1/4 windows. You'll need to pop this out (The Black GT Quarter window frame) to get to the 3 (and one mini screw bolt) on each side that directly hold the clip on and are hidden under the The Black Quarter window frame.
8. unscrew those 3 bolts on each side. Look closely, the third one is hard to see.
9. pull back the cloth and you will find three nuts on the roof of the car in the rear. pull the plastic surrounding off of them and unscrew.
10. On each B Pillar (or the piece of frame that holds the seat belts and side speakers) there are two holes right next to each other, one larger ontop and one smaller on bottom. You will need a 3" extension and size 11mm deep socket to get this nut off. it's hard to get to but if you feel around for it *it's about 1/2" above the hole" you will get it off no problem. Don't lose your socket down the hole.If your Quarter Windowes are old remove (use gloves) and the bolt heads can be easely ground off (this is an alternate way of accessing the B piller bolts)
11.It helps if you hold and lift udnerneath the and pull up while prying directly underneath the roof panel with a screwdriver at the top of the roof line because there are about plastic nubs that help hold the rear on. Good luck)"
[This message has been edited by James Bond 007 (edited 02-20-2007).]
[This message has been edited by Bubbajuju (edited 02-05-2008).]