So after much gnashing of teeth, yelling and everything else involved with this project the physical build is complete and as you can see there is a PCI card in there now.... There was no way around it ASUS has a failure somewhere and I am not gonna keep replacing the board to get the network card to run at proper speeds.
http://forums.nvidia.com/index.php?showtopic=103581
http://vip.asus.com/forum/view.aspx?SLanguage=en-us&id=20090508002440534&board_id=1&model=M4N78%20Pro&page=1&count=22
The above two links describe the problem I was / am still having so if you know the answer please contact me! From what I have read and seen the only answer is to replace the board.
Final parts list:
3x Seagate SV35.5 Series ST31000525SV 1TB (Raid 5 Virtual Machine Storage)
2x Maxtor DiamondMax Plus 9 200GB (Raid 1 OS)
HP dvd840i DVD Writer
ASUS M4N78 PRO aka the bane of my existence
3Com PCI 3c905C (if you don't know what this is... you have no business looking up parts)
AMD Athlonx2 7750 Black
4x OCZ OCZ2P8004GK 8GB total RAM
Enermax EES620AWT 620W
Logisys CS888UVBL BLUE
Okay and for the geeky details portion.
OS: Ubuntu 9.10 + Vmware Server 2.0.1
Software raid all around the primary OS is Raid1 between the two 200GB drives. The VMWare images are stored on the TB drives in a RAID5 setup with ext4 and lvm. It's purdy. I tried every flavor of *nix before I had to settle for Ubuntu as well. The original idea was RHEL because of its long life cycle and I would get updates free through work. Unfortunately RHEL, Fedora, SUSE all had problems seeing the drive controller correctly. For what it is worth I had trouble even getting this board to run windows correctly. Last to any of you Ubuntu people out there when someone is installing and selects a partition on a disk to be bootable it isn't necessarily always going to be HD0!!!! FIX YOUR INSTALLER! That little burp had me for a while and it took much hair loss to get it correct. I ended up having to disconnect all the sata devices with the exception of the DVD drive to get it to load the bootloader onto what I wanted because for whatever reason it decided that sata came before pata and kept loading the bootloader onto my raid5 set.... hate you guys, really.

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