Step 3: Drill holes and assemble
I think the easiest way to drill the holes is to line up your lumber and clamp it together, then drill through multiple 2x4s at one time. Even if your measurements aren't perfect or the holes are askew, at least the bolt will fit through smoothly, which is what's important. I discovered this technique halfway through construction, so some of my beams did not line up perfectly.
When you're finished drilling, keep the clamps in place and insert the bolts. Be sure to use washers on both ends of the bolt. I used a mallet to pound the bolts in, which helped speed up the process.
If you need to take the bolts out, don't make my mistake of hammering them out from the threaded end - I ended up ruining several bolts by hammering the threads away, making it impossible to screw the nut on.
View the photos to see where I drilled the holes.