Interesting note for someone in the future (probably me if I ever have to reinstall this MD)
the steps located at: http://wiki.linuxmce.org/index.php/Unrecognized_NIC
are partially incomplete (at least for my motherboard)
the atl1c driver is a little different in kernel < 2.6.34 and it would seem 1004 is running 2.6.32
So i had to apt-get install kernel-image-2.6.35, then run /usr/pluto/bin/Diskless_BuildDefaultImage.sh NOT mkinitramfs -d /etc/initramfs-tools-interactor/ -o /tftpboot/default/initrd (which gets run anyways inside the previous script Diskless_BuildDefaultImage.sh).
the trick was I had to remove the directory /lib/modules/2.6.32 (the previously installed kernel). Then running /usr/pluto/bin/Diskless_BuildDefaultImage.sh once the first part of the md install was over I had to follow the directions at the link above and add proper symlink in /usr/pluto/diskless/<md id>/initrd.img and vmlinuz