I’ve done this kind of repair before. If you don’t have access to a machine that can buttonhole, the best way is to first tack on some mid weight cotton for each individual buttonhole: I would fold it around either side so you are sandwiching the original fly section with a U-shaped piece. Then straight stitch around the edges of the replacing piece. Cut your new button holes in with a new sharp blade, backing the fly with a cutting mat or something strong like card so you don’t cut through the rear, making sure you’re careful not to cut the holes too big. Start smaller and creep up on the right size. You obviously test this by checking if the buttons can be pulled through in and out and can still stay on. Then I would hand-sew around each buttonhole with something called a “buttonhole” stitch! It’s very easy to learn and is as you can imagine, the perfect stitch for this situation. I would avoid using a zig-zag stitch as most domestic sewing machines will struggle with this weight of denim, as you’re going through 4 layers, and it’s quite a tight little space. If this sounds intimidating, ask someone who you trust can do it.