To vary the fan speed, the voltage is toggled on and off, with the duty cycle representing the fan speed. The problem is that on your motherboard, pin 4 uses the Intel fan control standard. Pin 4 - Speed control pin (1V = slow, 5V=moderate, 12V=jet engine fast) The pinout for the MacPro fan looks like the following: It's been a few years since I built my box using a 2009 MacPro case, but if memory serves, here's what you do: That being said, you can get it run with just a few simple tricks.
The fan in the MacPro case isn't really compatible with an Intel based motherboard. My apologies for posting to an old thread, but since you haven't received a reply, I'll provide a description for the benefit of others who may read this. Building a CustoMac Hackintosh: Buyer's Guide
