Cabling at the bottom of your case will be impeding the airflow from the bottom fan,
Mount your HDD the other way round and route your SATA power and data behind the motherboard tray.
The HD Audio/AC'97 is for your front panel headphone and microphone jacks; if these are unused you can unplug it provided you have somewhere to hide the cable.
Thanks; what is bclk pls?
Also does anyone have a view on which way my fans should be blowing? Surely I want the two water cooling fans pulling cold air into the case and over the radiator?
Nice one redek, looking good, what multi are you on and at what voltage?
What graphics are you using in this system?