I'm no 'wizard', but if you closely examine the way those windows are fastened into the fabric, it should be possible to figure this out. I say this because the tops are not all the same, many different manufacturers and techniques. Yours is likely glued in between two 'flaps' and double stitched all the way around. Or, it might be just stiched in, or it could be heat-sealed.
For sure, there are only two ways to do this job: manually, with the top on the frame/car, or with a sewing machine designed for the job and the top removed from the frame.
It sure sounds to me like you want to do this without removing the top. Fair enough. You'll need to carefully cut every stitch all round to release the strip of plastic left in there. This will take hours and hours. Assuming it can then be removed without damaging the fabric, (that is, not glued in and/or heat-sealed), you'll then need to cut your new plastic to size and insert it into the old top fabric, maybe held in place with some flexible glue.
Now, you need to address the thousands of little holes in the fabric made by the old stitching. I guarantee they won't line up on both sides. For a presentable finish, and to firmly hold that new window in with even pressure all round when the top is put down and then up again, you'll need to manually use a needle and thread and re-stitch through all the old holes left by the previously removed thread. Many, many more hours of hard work.
In the end, what you'll likely have is s**tty looking top windows with wrinkles and puckers due to the impossibility of manually getting every stitch tensioned and positioned just right. My wife has a walking foot heavy duty sewing machine capable of stitching through 2 - 3 layers of leather. For anyone to duplicate the actions of this type of machine by hand would be remarkable.
Now, of course, you could remove the top from the frame, cut out the old window plastic stitches by hand, as described, and then use a sewing machine to stitch in the new plastic...but guess what, you won't be able to hit those little holes again, which will now look like perforations all round the window. And, you will not be able to remove that old top without mucking up either the glued-on front or rear bows, probably both.
Sorry for the length of this, and I am not trying to rain on your parade, but I hope this explains fully why window replacement is simply not feasible. I know, it's a shame when the rest of the top is in great condition.
I just paid for new A/C condenser, and asked why a pinhole leak, caused by abrasion from an accidented crossmember, couldn't be welded when the rest of the condenser was mint. It's just the way it is. Sometimes replacement is the only option.

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1986 560SL
2002 Toyota Camry
1993 Lexus