So the footswitch and the relay seem to be working. The only thing that seems to not be working is the function of the red LED. Why don’t you go ahead and finish calibrating the pedal and soldering the jumpers…see if everything works except for the LED.
Since you know the actual LED is working (from when your multimeter powered it on during the diode test) and properly orientated, the problem is probably with a solder joint either on the LED itself, R11, or on the microcontroller…check pin 6. Make sure R11 is the correct value and there is continuity from one pin of R11 to pin 6 of the microcontroller. Test to see that pin 6 is going high (to 5 volts) when the LED should be on…measure this on the pin of the microcontroller itself, not at the socket’s solder joint. Make sure the microcontroller is seated properly in it’s socket.
It’s got to be something simple like this. The microcontroller is almost certainly working properly.
Good luck.
-Brach