I’m not sure what’s going on with the voltage on R28. Please check pin 17 on the microcontroller for 5V (Google “pinout for atmega328p” if you don’t know where pin 17 is). Let me know what you find.
It’s not super vital that the silencing circuit works; it’s job it to help make the relay click quieter. So unless the sound of the relay click bothers you then you don’t need to worry about fixing it.
Is the gain trim pot set correctly? You should have more than just unity gain with the volume knob all the way up. You might want to play around with the gain pot setting to see if you can increase the volume. If turning it (all the way counterclockwise) doesn’t help, try gently wiggling the gain pot (while playing guitar through the pedal) to see if that makes the volume jump up to a louder level.
-Brach