I arranged the 4 pieces in a stack as pictured. I marked the top pieces and the bottom pieces. The I used a speed square to mark the center lines of each piece and approximately where the holes would go.
But approximate is not good enough! I inverted the stool (sans seat) and lined the holes in the flange up with the center lines on my 2x4s. I centered pieces of wood under the flange as best I would, and then marked the holes on the wood with a pen.