I just check the Clean code and it works... BUT only have sound when RV1 is full left. Before it's a kind of very very faint clean signal with noise even when used with power supply. The sound dramatically drops until it's not at full left position. It looks like not enough signal went off the opamp and 500K is too much for leveling the faint signal.
The RV1 resistor timer acts in an "exponential mode" (it's not perfect but makes the circuit much simpler). That means that the last part of the swipe contains almost all the action, so it is normal to feel the change at the end of the pot turn.
Regarding pin 5:
you would also need:
www.electrosmash.com/images/tech/pedalsh...-MEGA-start_pcbs.jpg
From the voltage divider, it is normal to lose some level over R2 and R3. Could you compare your voltages with the ones I am measuring?
What are the R2, R3, C2 V values ?
you can see them in the image above
Please check those voltages and let me know, seems that your pedal is almost working. Looks that maybe the guitar is not reaching the op-amp properly. It would be great if you could measure the guitar signal at pin5 but I understand that not everybody has access to an oscilloscope.
It would be interesting if you can send me a photo of your build especially of the op-amp area.