The good news is everything else is working fine, so this LED should be too hard to fix…in theory.
First of all, R11 should be hooked up to the LED cathode (the round pad), not anode (the square pad); and the LED anode, not cathode, should be hooked up the the U1 pin 6….please note the schematic. Reverse your hookup wires and see if that fixes the problem.
If not, re-seat the microcontroller in it’s socket to make sure there’s not something wrong with one of the pin connections.
There is a chance that the LED could be in backwards. Using your diode tester on your multimeter, with the red lead on the square pad and the black lead on the round pad you should get around 1.7V across the red LED (and around 1.8V on the green LED).
You can just run a jumper from pin 1 of the microcontroller to it’s pad. Pin 1 is the reset pin so it shouldn’t matter for this LED problem…but you do need to hook it up to keep your pedal from resetting every time pin 1 drifts low.
Let me know what you find with the LED.
-Brach