Weather strip on FG rear deck lid

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You'll most likely have problems. In my experience the space for the weatherstrip is waaay tighter at the rear than at the front -- it's not a consistent gap like with a stock steel decklid. If you use the stock weatherstrip you won't be able to get the decklid to close far enough to fit right with the quarters and quarter extensions, and if you use something thinner it won't be thick enough to seal along the front edge.

This was my experience with a Shelby-style decklid, and there are many brands of 'glass out there. YMMV. Look at the 9,000 mile original '67 GT500 in the August Mustang Monthly and you'll see the decklid sitting 1/4" higher than the quarter extensions. This is how they were from the factory and I've seen it countless times. The best thing to do is to put the decklid on the car WITH WEATHERSTRIP before paint & body and rework the decklid & quarter extensions to fit right.
 
Reenmachine--did you use any trunk weatherstrip or any special brand? The body shop is fitting my doors and trunk lid now and asked me for the weatherstip pieces. If they put the weatherstrip on before paint wont they have to be removed and reinstalled after paint? Probably would be destroyed if removed. Who makes the best weatherstip products? Thanks
 
I've always used whatever weatherstrip K.A.R. Auto Group stocks. Yes, order two sets of trunk weatherstrip at the same time so you're sure you have two identical sets. Consume one as part of the bodywork, and then install the other during final assembly.
 
I had no trouble on mine. The weatherstripping easily compressed into the gap on my Branda decklid. Does it seal? I have no idea, the car has yet to be wet. I installed the trunk bumpers when i did the bodywork on my trunk and endcaps for the very reason reenmachine mentioned. I was determined that my trunk and end caps would fit perfectly. By latching the trunk tight against the bump stops and jacking the hinges around, my trunk fits better than the original steel Mustang deck lid.