Convertible top leaks into area behind backseats. (1999 Mustang GT)

Recently purchased a 1999 Gt convertible. I have noticed that when it rains. the water leaks in from both ends of the convertible where the straps are. The water then pools in the leather pouch behind back seats. What can I do to fix this? Drain hole? Flex Seal? Flex Tape?:(
 
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Inspect the rear wind screen in the lower corners by the glass. Look to see if that's where the water is coming in. If so replace the top rear wind screen.

What happens is the repeated bending of the fabric creates a weak spot in the fabric. The bend is always in the same spot because of the glass. Once it wears through there's a leak. I tried a ton of DIY repairs but in each case I found that there wasn't enough fabric for the patch to stick to. And when I did get it to stick the patch itself would come off from the folding of the convertible top.
 
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^^^^I'm about to order a rear window for my 2k...repairs (as wmburns points out) do not hold. That said, there are videos on YouTube about what to look for if you wish to try a repair...
 
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There is a seal underneath the area where the top bolts on, it’s $36.My car had leaks on both sides in the same spot, the seal has double sided tape to fold over the lip, there was a 3-4” section on both sides that was dry rotted and allowing the water in.You could watch it trickle in the corners while it was raining.Its called the retainer plate seal, I ordered it from parts depot and it’s an OEM part.You can see in the pics the sections that are bad, I’ll put the original and new to show the difference.
 

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My and my dad had this same problem in his 03 cobra!
Look under the car for the factory drain. There is a little seam were the water is supposed to come out. Mine was pinched to small. I used an all and a little hammer and opened it up some more. Water drained out for a couple minutes.
Try that