If you're going to use molex connectors, might as well tap it right off the PSU.
I have some question about using 3 pin fans on a 4 pin board socket. That's a "PWM" tap.(Pulse Width Modulation).. The output may be null with a 3 pin fan connected.
But really, when you get to that number of fans, (especially 3 pin units), the best approach would be to take the power directly from the PSU, and route it to a fan controller panel.