Disclaimer: I know nothing about stompboxes, or troubleshooting them. That said, I'll try to help.

My voltages:
Q1 & Q2: C -3.8v B -1.52v E -1.49v
Q3: C -3.2v B -.06v E 0v
Is it odd that Q1 & Q2 have the same base and emitter voltages? Q2's base should be the same voltage as Q1's emitter (since there's a direct connection), and the two transistors are biased differently. Q1 has the 10kΩ emitter resistor and two resistors setting its base voltage, but Q2 uses a different emitter resistor and its base is pinned to Q1 emitter. I don't know what's typical for this circuit, but I'd have guessed Q1 and Q2 would have different emitter voltages (if only to bias Q2 on).
Disclaimer: I know nothing about stompboxes, or troubleshooting them. That said, I'll try to help.

Interestingly, when the pedal has a buffer in front of it (in my case, a TU-2), it sounds perfect. I can clean it up with my volume knob, and the tone knob works as it should. All the high end is retained through the full sweep of the guitar's volume knob.
What is the buffer doing to clean it up so well? ...
Is it normal for a MkIII Tonebender to work well with a buffer in front? Did you use Germanium transistors? I ask because I thought the conventional wisdom was a buffer in front of Germanium makes them sound harshly bright...
Got a clear photo of your board?
I wonder if Q2 has the correct orientation of emitter & base (different than Q1). If Q1 & Q2 had their emitters connected, and Q2's base attached to the 3.3kΩ & 10µF, that could cause some weirdness...