You can test if the LDR is working by unsoldering the jumpers (JP3 and JP4) and measuring the resistance across TP3 and TP4. Keep the depth knob off and the resistance should be relatively low (when the power is on). But you should have already done this when you calibrated the pedal, so I would guess that it’s still working.
When you measure the resistance between R15 (the pin of R15 closest to pin 1 of U2) and pin 3 on U2, what do you get (with the power off)?…I’m wondering if S5 is working properly.
Also, what DC voltages do you get on the pins of U2A, pins 1,2, and 3?