Wow, a very complex pedal - makes it tough...
At the very least, I would visually inspect all parts & solder connections that receive physical stress - stompswitch, jacks, pots. Perhaps touch/apply a little pressure to those connections carefully w/ a small tool or tweezers, looking for a loose connection. Verify that the in/out jacks are ok - i.e., clean connecting pins, not dirty, not bent. And look closely at that ribbon connector to the stompswitch - signs of wear, bad connections, etc. It doesn't look like there's any PCB cracks...
Did you search online (@ MXR Forum, DIY stompbox forum, etc) for others with the same problem?