With your signal probe do the following checks...
You should have signal at both ends of C1, R2 & R3.
You should have signal on the left side of R7. When you pluck a string with the probe on the right side of R7 you will get a squealing sound. You will also get the squeal at pin 2 of the op-amp. Don't have your amp turned up very loud for these squeal tests.
With the toggle switch set to AUTO mode place the probe at pin 1 of the op-amp. You should get a wah sound here. You should then hear the wah sound on both sides of C4 & C5.
Next go to pin 5 of the op-amp. Here you should get your normal guitar sound. You should also get the same sound at pin 6. At pin 7 of the op-amp you will get a much louder guitar sound.
The signal should now be at both sides of C7. You should next hear your guitar at the bottom of diodes D1 & D2. You should hear a distorted sound at the top of D2. You should also have this distorted sound at the bottom of R13. The sound at the top of R13 will be much lower in level. This same sound will also be at the wiper of the LEVEL pot as well as the left lug of the toggle switch. It will also be at the center lug of the toggle switch when it is set to AUTO mode.
Here's an update on the voltage for the Opto-Coupler's LED. With the toggle switch set to MANUAL mode you should have about 1.5V on the + lead with the MANUAL knob turned fully CCW. With the knob set fully CW you should have about 1.4V at the + lead. With the toggle switch set to AUTO mode you should have about 0.8V at the + lead regardless of where the MANUAL knob is set. Since your voltage wasn't near these values check to make sure you have a 10K resistor at R16.