Hi,
Thank you all for good avice and excuse me if I'm asking for something obvious.
I built an almost identical system. Everything works 100% (including sleep and USB 3), with the exception that the fans seem to be running at full speed all the time. This makes the system very noisy and I think I could afford to reduce the fan speed, since the CPU temperature is around 36 C and system temperature 40 C. I have enabled smart fan control in the BIOS and tried FanControl
http://www.macupdate.com/app/mac/23137/fan-control and smcFanControl
http://www.macupdate.com/app/mac/23049/smcfancontrol. Neither worked and smcFanControl did nothing after stating that it has not been tested on my system.
In the install, I used iBoot+Multibest with custom DSDT, 64 bit GraphicsEnabler=yes, Lnx2Mac's RealtekRTL81xx Ethernet, realtek audio kext and USB3 kext.
I hope I have provided enoiugh information for someone smarter than me to spot the problem. Thanks in advance!