The pin 3 / 6 swap doesn't matter for this board. They both tie to ground on the power supply.
What Williams *should* have done is tie solenoid ground to both pins 2 AND 3 using paralleled wires.
And they should have also tied lamp ground to both pins 5 AND 6 using paralleled wires.
This would have helped J2 to be a bit more reliable but J1 would still be a PITA.
Now ... if the one going the the lamp circuit is the one that shorted, check for shorted lamp sockets/wiring.
Maybe too large of fuse?