What about all the other wires that go to your motherboard's I/O plate? LAN, audio, USB, eSATA? You have that INSIDE the desk... going to be a pain to plug in a thumb drive, or replug a speaker.
Hmmm. The audio I will probably be getting a DAC or something so I would just have the audio going to that and then plug into that whenever needed. Also I am planning on getting a USB 5.25 bay or something to install into the front of the desk. Not sure about E-SATA though. Not too worried about that though because I currently dont use it for anything but I could see that being an issue. I seriously appreciate all the help and It does make sense to turn the motherboard because it would be much easier to use the PCI-e extenders since they will be on the same plain. Going to do a complete redesign tonight or tomorrow and post the update when I get a chance.