did you try pwm settings in bios ?
The BIOS doesn't provide HDD temp as a temp sensor to control the PWM fans, only the CPU and the Motherboard temps are options.
I was finally able to get SpeedFan loaded on the server but I don't think it is sensing the PWM fan speed. This MB has a single PWM fan header other than the CPU fan header (4 pins vs. 3) I have 3 fans connected to this header via two Y PWM fan connectors that came with my Noctura Fan's. Is this a configuration that will work in the way that I am trying to get it to work?