I think you'd be better with an external PWM plug (an extender) and software control your fan speed (like fancontrol on Linux). An Arduino on an internal USB header could also generate the PWM signal if you can't control the motherboard directly.
Deep down the idea of having to have a windows software driver for my computer fans and some crappy piece of software to talk to them over a crappy propriety protocol appeals to me about as much as amputating my own toes w/out anaesthetic w/ a blunt axe. to each their own though i suppose