Thanks for the response. I took the calipers off and checked the action of the pistons and pins - everything seemed to be in order. But when pushing in the secondary master cylinder with the LF caliper off, I realized that I could push it in with no resistance. This seemed odd, and pointed the finger at either the SMC, or at something in between it and the rear caliper.
I went ahead and bled the PVC. Last time I did it, I removed the caliper, angled it and then used a vacuum pump. This time, after first using the vacuum pump, I also did it manually, having a friend actuate the SMC as though it were the lever or the pedal, while I bled the PVC. It worked wonders - the lever now generates all the force I would expect, and slows the bike down in a hurry. The rear is now much improved; the pedal isn't rock hard and actually moves a fair bit, but the braking force still isn't what I'd want.
Next: I suspect the rear pads might be contaminated by the grease I apply to the back of them. It's a pain to get those rear pads in, and I dropped them/messed up several times and definitely got grease on them. I am going to switch out one of the front pair with the rears and see what that does.
Additionally, I didn't fully bleed the pedal circuit this time, just the PVC. While that was probably the issue, I really should do the entire pedal circuit.