I've put 14" YKK coil zippers available in most fabric stores, even Walmart, in cycling jersies and windbreakers by simply ripping open the seam with a seam ripper. Then I first attach the zipper by the edges with a zig-zag stitch one edge at a time, right sides together, leaving the ends unstitched at this time. Turn the garment right side out, open the sipper, then topstitch a box around the entire zipper. Rather than snip a Y into the ends to get a clean rectangular box of stitching, I usually just taper the stitching down to the original seam so this top-stitched box of stitching is really a hexagon. All this this could be done by hand but is slow. With a sewing machine, ripping out the factory stitched takes lonegr than sewing in a pit zip.
A cleaner installation involves sewing a zipper neatly into a gusset then sewing the gusset into the ripped open seam. This is useful for instance where you want a flap over the zipper, the flap material can match the gusset and look like it was original.
You could bind the seams that scratch with grosgrain tape or lycra that is used to finish the cuffs and edges on some fleece garments.
No experience with windstopper. I prefer seperate wind and base layers for layering versatility.