Either way, I've now got the system running, but not without some serious battle scars.

Ubuntu happily installed (very slow to partition/newfs stuff though). However, upon reboot, the bios clearly couldn't see the boot drive. My SATA drives are plugged into the on-board Silicon Image RAID controller with no raid configurations set up.

Guessing, I told the raid controller to create a 1-disk concatonation with the disk I wanted to boot from. Voila, the BIOS sees the one disk now and I can boot from it. Linux finds the other two SATA drives when booting.

Sigh..

Also, when Ubuntu says "Computing the new partitions" it really means "I'm creating a new partition right now. Go get something to eat, I'm going to be here for a while." Large partitions, for some reason, take quite some time to create.