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.
The fan in the MacPro case isn't really compatible with an Intel based motherboard. That being said, you can get it run with just a few simple tricks. 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:
The pinout for the MacPro fan looks like the following:
|______|
| 1 2 3 4 |
Pin 1 - ground
Pin 2 - Vcc, or 12V
Pin 3 - Tachometer sense pin
Pin 4 - Speed control pin (1V = slow, 5V=moderate, 12V=jet engine fast)
The problem is that on your motherboard, pin 4 uses the Intel fan control standard. To vary the fan speed, the voltage is toggled on and off, with the duty cycle representing the fan speed. So if the control is on for a 1/4 of a second, and is then off for 3/4, the fan would run at 1/4 of full speed. The Mac Case fan wants an actual voltage which would be on continuously at ~3v for the same quarter of full speed.
The simple trick is to use a small knife and squeeze the retaining pin on the Pin 4 plug connector. The Pin 4 wire will pull out of the socket. If it doesn't slide out easily, you aren't squeezing the retaining tab in the right spot. One pin 4 is out, you can safely plug the socket into an Intel motherboard fan connector port. Everything is ready to go, you just need to apply a voltage (0 to 12V) to the speed control wire that you just release from the connector. A good source is to tap straight from the Power Supply Unit (PSU) using one of the +5V pins from an unused disk drive molex connector. If all is well, your fan will be spinning at a good rate, and you can go into your BIOS display to see the actual fan speed.
My ASUS rig has a few of these fans running using 5V for the fan speed setting. There is plenty of cooling for a 2700K CPU, and I haven't really found the need to increase the fan speed. Someday, if I want to overclock the system, I could implement the variable speed feature. This would require building a small circuit to convert the motherboard pin-4 speed signal (pulsed on/off) and generate a continuous 0 to 12V signal that would feed into the MacPro fan. The general approach is to use the motherboard speed signal to drive a transistor, which acts as a valve to vary a 12V power source. The output would be a pulsed 12V signal. You'd connect the oscillating 12V wave to an appropriately sized capacitor to smooth the output into a stable voltage. The stable output voltage would then feed back to the fan to control its speed. The result would permit the pulsed motherboard signal to vary the MacPro fan speed.