I replaced my top this past October. I have to say that it was not nearly as intimidating as it is made out to be. I made good use of three specific videos on YouTube including the one mentioned in the above post. I looked at my window closure last night and I honestly cannot see how you are getting the window to crush your seal like you show in your photo without some major misalignment of the seal. That's just crazy. It's easy enough to remove the front and side seals without disturbing any of the top material whether it was glued or taped. You could do this and reassemble based on the videos to see if something were reinstalled incorrectly.
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