One of the legs of R1 is in the wrong solder pad, I've marked in purple which leg it is and which hole it needs to go in (
).
Fix this and report back.


Suggestions:
PROBE ITBuild an audio probe and use it to trace the signal (google it). If you were using a probe, you would have found out that that the signal was not actually making it to the first transistor (R1 being on the wrong pad), and you would have worked this out quickly.
SIMPLE IS GOODUnwire the circuit from the stomp switch - just have the straight inputs and outputs and no other distractions. Make sure the circuit is working before wiring up stop switches and boxing. At least this way you start with a working circuit, and if in the process of boxing it up new issues appear, it's not the circuit, it's off-board issues.
BREADBOARDIf you plan on building a few, buy a cheap breadboard and you can use this as a test platform.