Step 1: Rough mill the 2x4s
First, on the miter saw, I squared off one end of each 2x4 and then cut them to 6' They were roughly 3 3/4" thick. I used the table saw to rip 3/16" to get each plank to 3 9/16". (Later, I will take off another 1/16 using the planer.) After all that was done, I spent some quality time with the orbital sander. I first hit each one with 120 grit and then again with 220. The main goal was to clean the surface and maybe get some of the splinters out. In hindsight, I should've cut them a little longer than my desired finish length, but everything worked out.
Step 2: Drill the holes
Using a 3/8" bit in a drill press and starting 2" in from the bench end, I drilled five holes 17" apart. (This is just how the math worked out.) The holes are meant to be visible from the front.
I used the holes to run threaded rods through the bench, front to back, to hold it together. I used 5/16" rods, so using the 3/8" bit gave me a little wiggle room. For the front and back end pieces, I also used a 1" forstner bit to drill through about half the thickness of the wood. This allowed me to inset a nut with a 1" washer.
After one sort of rough go at locating the holes, I made a template out of scrap 3/4" OSB and used another strip of OSB as a shim to consistently space the work in the drill press vice.