Greg,
How this system works is this - The latching controller has four connections, one +12 VDC, one -12 VDC, one for all of the switches and one for the load.
When you turn on anyone of the switches, the switch indicators should light up unless the bulb is blown in the switch itself or the indicator lamp.
The latching controller will send 12 VDC to the load terminal which is connected to a HD relay and activates the relay.
The HD relay will have a larger HOT wire that should be a good constant +12 VDC which when the relay closes, it sends that +12 VDC power to the pump motor.
The reason for the HD relay is because the Latching Controller can NOT handle the amps needed to drive the pump motor. So they use a secondary relay to handle the higher amps.
You need to verify that good power is present at all of those places and if not, why.
Are you sure that you got the relay wired correctly?