The first time I removed my back window I had a hell of a time, first the driver side zipper was frozen, and I was also without that last zipper piece, the silver piece, so I had to kinda just push it back in there and hope I got the zip right XD
But I just unzip to the driver side and give it a tug it usually just comes out, maybe look into some form of zipper cleaner/lube they sell them for your soft top.
Did you roll up the back window and take the top down? did that ruin your window?!