Yeah I have an S500 with treble and bass control. Still useful sometimes but much more useful on my Reverend with revtron pickups and my Novo with P90s.
The solder joints look good to me. If this is consistent the short must be very obvious. Do you have a metal bezel touching some traces or something like that? I had that problem once.
I don’t have a way to draw a diagram at the moment. You basically keep the A/B switch the same, but the two green wires would both go to the top left and right pins on the master bypass switch. The middle left and right pins of the master bypass go to in and out and the bottom two are connected...