I’m glad you enjoyed you Quaverato build, but that’s too bad about it not working yet.
Are you saying that the signal is bypassed through the pedal no matter if the red bypass led is on or off?…as in you can hear the guitar signal on the output jack at all times? If that’s the case it sounds like the signal isn’t even going through the effect circuit…like the relay may not be switching properly. The jumpers would only matter if the signal was going through the effect circuitry. Don’t worry about jp2 for now, we can always bypass that with a jumper.
If you could send me some (detailed, in focus) photos of both sides of the board to info “at” zeppelindesignlabs.com (if you can’t find a way to post them on the forum), I might be able to see something. Pay close attention to the solder joints of the realay and the microcontroller. You may also want to re-seat the microcontroller in it’s socket to makes sure there’s no problems there.
Good luck.
-Brach