I have opened a vsd6 controller and here is how its connected up. The circuit board looks the same as mine so presume that its the same contoller. (Its the later digital controller that has 3 battery charge bars.)
The first black one on the right of the photo closest the capacitor is negative to the pump. It would also be black with the original wiring so would be wired up to the black wire from a Shurflo pump.
The second grey one in from the right side is the positive to the pump so would be connected to the red wire to the motor by-passing the pressure switch.
The third grey wire from the right is the positive in from the battery.
The fourth black wire on the left of the connector is the negative back to the battery.