I have a Thermalright Ultra 120 Extreme in my Microfly...it's really not that big of a deal. What saves you the most space is actually moving the hard drive to the second optical bay. Also, modular PSU is key...
i would try wake by PCI devices...technically, the internal network card is a PCI device, even though it's built in.
also, under device manager in windows, go to the nic's properties...under advanced, turn on "wake from shutdown" and under power management, turn on "allow this device to wake...
Are these too high? (CoreTemp temps in parentheses)
T = Speedfan (CoreTemp)
Tload = 42 C (57 C)
Tidle = 27 C (42 C)
Tambient = 26 C
No OC, everything auto.
Setup: E4300, XP-120, Microfly with extra 120s (1 in, 1 out), HX520, P5K-VM, Ballistix, new bios (0601?). Thinking my XP-120...