It's still not clear what transistors you are using. They seem to be plastic 2N2222A's. I'm in 100% agreement with duck_arse. The plastic package implies a PN2222A or a P2N2222A, those two have opposite pinouts. A plastic package 2N2222A has an ambiguous pinout. If I had to guess I'd probably go with the PN2222A pinout, the same pinout as the 2N3904. That's the way you have wired them up (ie. opposite to the GGG documents; the GGG documents are unclear unless you already know then answer!) The On Semi P2N2222A should be marked with the preceding P on the package but the pics of the device you posted earlier do not show a P.
Let's assume the pinout is correct for now. The signal trace of the PCB shows a signal on the emitter of the last transistor Q6. That means we should be getting some signal out of the unit. But the symptom is we are not. The signal is getting into the board, since the signal trace works, but it's not getting out. Beyond Q6 we only have to pass through C16 to the terminal marked "O" at the top right of the layout,
http://generalguitargadgets.com/pdf/ggg_superfuzz_lo.pdfThe best thing to do would be to signal trace each side of C16 and the "O" terminal.
To me it looks like there is a problem with the wiring of the footswitch, or the footswitch itself. The fact you can bypass means the output socket wiring is probably OK. Maybe a photo of those would make it clear [found some, see below]
If you want something to try you can connect the wire from the "O" terminal directly to the output socket "tip". You should hear the signal you are getting on Q6 emitter/C16/"O" terminal on PCB. That would show the PCB is working.
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EDIT:
I scanned over the thread and the footswitch wiring pic you posted earlier looks OK. The wire going between the "O' PCB terminal and the footswitch is the dark blue wire. The signal is getting lost somewhere between Q6's emitter and the footswitch. Maybe try resoldering C16. You can also use the audio probe around the footswitch wires. if you get a signal on the dark blue wire on the footswitch maybe the problem is the footswitch soldering or the footswitch itself.
