It is more likely a problem of the fuzz oscillating when it is bypassed, because its input is left floating by the true bypass looper. Grounding the input of the fuzz when it is bypassed (with the throw of the switch also used for the LED) should stop it from feeding back on itself.
I think that's exactly what I need to do, I just can't figure out in my head how to accomplish that with the switch (it seems like all the throws are taken up with having to account for the two individual loops send/returns/LEDs and the in/out of the box).
The 9 pegs of the 3PDT are set up in this fashion:
1.Return B 2. LED gnd B 3. Send B
4.Out 5. Ground 6. In
7.Return A 8. LED gnd A 9. Send A
What would you propose connecting in order to add that functionality? In just poking around with a piece of wire to try different combinations, anything that grounds the A loop while B is playing, also shorts out the signal when A is playing.