This does not correspond to what you reported. Just thought you had a measuring error on pin 1 on pot, being "close enough". Sounds like it fluctuates - but its stable on the pin without the molex connected, so that limits the problem area of that specific problem to the connector, the cable, and the pot
Can you show a picture of the pot with connector? Is the sequence correct? Does the measurement on pin 1, change as you turn the pot?
Measuring Threshold
On board:
Pin:1 +11.28
Pin:3 -12.01
On pot:
pin1: +9.91
Pin3: -12.05
Measuring Gain
On board:
Pin1: -12.07
Pin3: +11.78
On pot:
Pin1: -12.07
Pin3: +11.79
Could be - show a picture of the bottom of the board, pls.
Also, recheck resistance to -15, unless you did that before resoldering.
Gustav