Andy,
Sorry about this trouble.
Your idea to re-flow the solder joints was good. That would have been my first guess. I know that the problem has to be somewhere in the analog signal path…it could be anywhere from the beginning of the circuit to the output.
Does the signal sound fine through the pedal when it is bypassed (when the red led by the bypass footswitch is off)?
What are the results of your tests of step 6 in the troubleshooting guide?
-Brach