Sounds like somebody didn't get a clip...
You will first need to fool the ECU into thinking that the water pump is there.... Grab your diagrams and wire that stuff in. That'll keep the check-engine lights away.
The two thick wires on the connector are power for the pump. Black w/ white strip is power and White with black stripe is ground - though after the plug on the pump itself, the wire colors might not match the diagrams.
I just wired it all up as stock on my swap (took the wires out of the front harness). Later, I'll wire it in constant.
-Charlie