That’s very interesting.
Just as an experiment take the micro out of the socket and re-seat it to make sure it’s getting good connection on all the pins.
Is the Aref (analog reference) voltage on pin 21 a stable 5V?
Is it still exhibiting the same symptoms since you messed with the presets? If so, does moving each of the pots and switches (all of them) cause the pedal to behave normally?…as in the pedal snaps back to reality? From my experience when the eeprom has random values in it this pot movement causes the pedal to behave normally again….but powering it off and then on starts the weirdness again. This is why I had you sweep the pots.
Yes, you can re-order just the micro, but i’m not entirely convinced that that is the problem yet.
Let me know what you find.
-Brach