This would be an easy way to fix.
1. Remove wire from Main Board Ground to 3PDT Board +9v pad altogether (see Red X 1) and forget about it.
2. Remove wire from Output Jack Sleeve where it connects to the 3PDT board (See red X 2) and resolder it to a fresh ground pad in the OUT box directly above the T pad on the main board pointed at with blue & white arrow. This is another extra ground.
That is it.
Many ways to accomplish the same thing: For example you could do the same maneuver with the Input Jack Sleeve wire and connect it to the IN box Ground Main Board if that seams easier for you. Those are the easiest ways needing only one point of solder work.