Will an MPF102 work? Are they 100% the same as the PF5102 or just a reasonable substitute?
I have a ton of them, and in most circuits, they are too low-gain to be used as a common-source amplifier.
Looks like it might have been fried by overvoltage.
I wouldn't bother trying to troubleshoot. Put it in the 'save-for-later' bin and try to make another one.
Or connect the 3 pins of the toggle switch to the 3 holes for the pot, and put a 470k resistor across the switch.
Same result, but the wiring should come out cleaner.
If you have a way to cut it at the red line, that might be less noisy.
If the pop is bothersome, your next best option is to just disconnect lug 3 from the pot.
You figured that part out yourself, you just didn't need the left half of the drawing.
The downside of switching R1 is that you might hear the footswitch click.
Either method will be fine. Personally I would do R1 and run the wires to the footswitch on the left, and be very weary of picking up electronic noise from the logic chips. Those chips are flipping a square wave at over...
If that's all you want to do, all that's needed is cutting the connection to lug 3 on the pot; the left side of the DPDT switch you have drawn is unneeded.
Better yet, put R1 on the switch instead. It will kill the dry signal just as effectively. The benefits are
You can still use pcb mounted...
I settled on the CH341A devices sold on Amazon, and have it connect to the Pythagoras via 3.5mm headphone jack, much like varlogtim shows above. It's ugly compared to what PedalPCB had intended with the FV-1 Development PCB, but it works just fine.