I tried stitching the window as seen in the picture above, played that game for several years. My issue eventually became that the zippers base on the top itself came loose, the thread and some holes failed, thus there was no place to secure the replacement window's zipper.
The more I fixed the more it would loosen at another point because when you fix it, it becomes difficult to keep the load even around the entire opening, thus the top want to tear in places that are tighter than other parts.
I have officially given up hope of repairing the original top because at this point it needs to come off, and if you are going to do that you might as well put a new top on the car.
I am now looking at a complete replacement top in my near future and that's going to be about $1500 USD installed professionally.