I'd avoid the WD40 so near a window. Clear plastics and oil based cleaners don't go well together. You can check with some upholstery/vinyl/shoe repair shops about jammed zippers. Spray zipper lubricants might be the best chance to get it loose.
Are the windows hard to see through because of scratches? pledge will help a tiny bit but the only fix to heavy scratches is replacement. Try to give em a good wash first, and not removed from the vehicle on the ground. You will just be scratching the opposite side (I see this way too much).
I had the same issue on my 93 YJ with the button snaps. Heating up the top is the easiest way. If that doesn't work you can pull the vinyl, just pull it evenly so you don't rip anything.