Why would you change the 4pin connection to a 3? There is a reason why it is a 4 pin. The most obvious is for some kind of control. That 4th pin controls the speed and I'm guessing if it senses a higher temp runs the pump a little quicker. Unless there is no logic in the circuitry of the pump at all. It actually would have been easier for syscooling to keep everything 3pin, but I think the 4pin is there for a reason.
That's why you can't find any molex power boards with 4 pin connectors on them.