I can answer questions 2, 3 and 4 for ya.
There's nothing wrong with the set up. The CPU fan is temperature controlled. When you first start the computer the fan is switched off because it just isn't needed as the CPU is cold. So the BIOS will give this error due to the CPU fan not turning. This is standard on premium ASUS motherboards. My fan only just starts turning while Windows is loading, which is when the CPU will start to do something and heat up.
So nothing wrong with your motherboard or CPU and it just shows that the cool & quiet feature is working properly.
What I have done is turned of the error reporting in the BIOS so that it doesn't tell me that the fan isn't turning when I first boot up because I know this anyways. The other option is to switch off cool & quiet but the CPU fan will spin at it's highest speed all the time which would annoy me. Although you have a fan speed controller for the CPU fan and woud mean you adjusting the speed manually all the time.
I would connect the CPU fan directly to the CPU fan connector on the motherboard and use the speed controller for another fan on your set up because cool & quiet will adjust the speed automatically.
Do this to set up the 400GB partition: START>>MY COMPUTER
. Right Click on MY COMPUTER and Click on MANAGE
. In the bigger section Click on STORAGE
then Click on DISK MANAGEMENT(LOCAL)
. You'll see your partitions here but the 400GB will be blacked out. Right Click on the BLACK Partition and select Format Partition
. Once this is done you'll be able to use the space.
And I know the clicking noise your getting through the speakers. Like you said it's the same sound you get when you click on the back button on a browser. I think this is a software issue, driver maybe, though and nothing to do with your hard drive. Infact it might be a problem with the bworser settings.
If you have a spare CD drive kicking about then try using the 'old' CD drive to do the install.
Apart from the few 'issues' that are coming up with this set up, which is common with some new builds, you have a very sweet rig there!