I like to make all of my cutouts for longerons and other sticks that pass through bulkheads and formers by making the side cuts with a razor saw that don't go quite as deep as you want the final notch to be. Then use a chisel or some other tool to remove the unwanted part and finish off the depth with a sanding stick made from the same width material as the cutout. Sandpaper on the bottom side only.

This allows you to make very precise square corner notches. You can even make a depth gauge on the sanding stick so it's a no brainer to repeat the same dimension notches over and over again.