It's not the pedal bearings. I can duplicate the noise just by applying sufficient force just to the crank and the left side. Also, I checked the torque on other bolts nearby. Turns out the front derailleur was slightly loose, but tightening it did nothing.
As far as the BB shell being faced properly, this is one of my theories because when I set the torque on the dust cap, there's a certain point at which the amount of force necessary to turn the cranks (very light) is not exactly the same all the way around. The only thing I don't like about the facing theory is that I only noticed the noise recently and the bike only has around 4000 miles on it -- kind of long for a flaw like that to show, but not long enough for regular wear and tear.
One of the stupid things that I did when I removed the BB was that I didn't bother to put new grease on the threads and there was very little there. One of the first things I'll do is take everything apart and regrease just in case that's it.