Steps
I would love for you to explain what you did
Alright these are the steps I took:
1. I ordered the system with the 320 GB drive but bought 2 1TB Seagate drives so when I got the Mac Pro I setup the 1 TB drives in a RAID 0 set and reloaded OS X onto them. In doing this I moved the 320 GB drive to bay 3.
2. Once reloaded, I used the DiskUtil program in OS X to erase the 320 GB drive. I told told DiskUtil that I just wanted to use MBR on it which is what Windows expects and Linux is used to (though I think Linux can also handle the Mac partitioning method too). I created 3 partitions on the drive of around 100 GB each and created them as FAT32.
3. I did a reboot with the XP install CD and held down "C" when rebooting which made the Mac boot off the CD. I did a basic install of XP to the first 100GB partition telling it to reformat is as NTFS. Didn't really have to do anything special here. When done and the system reboots you need to hold down the Option key to get a list of drives to boot from. Should be one labeled "Windows" and if you boot from this you get into XP.
4. I then did the same thing with Vista 64 Ultimate. Boot from the CD and tell it to install in the second partition on the drive. When done I tested that I could boot off the drive labeled "Windows" again. It put me into the Vista boot loaded which gave the option of booting into an "Older version of Windows" which was the XP or into Vista. Two down, one to go!
5. I had to use the alternative AMD64 CD to install Kubuntu. The desktop install CD wanted to use an old nvidia driver which didn't like the 8800 GT in the Mac and it also seemed to cause crashes with KDE. So burn the alternative install CD and put it in the Mac and reboot and hold down "C" to boot from it. You end up in the grub bootloader for Linux and have the option for a Text install (which is the default). Pick this choice but press "e" first to edit the boot params and then edit the line with the kernel that has "splash" on the end. Remove the word "splash" from the boot line and then press "b" to boot. Note that this removal of "splash" was needed with the 8800 GT but may not be for other graphics cards.
You should get to the text based installer and be able to go through it all just fine. Everything installs and in the end the system reboots. Along the way it replaced the boot loader in the MBR with grub with the ability to pick to boot Linux or go to the Vista boot loader and pick XP or Vista from there. The problem is that none of these work anymore! The grub setup that the Linux created is wrong. Or at least it was wrong on my system and its wrong because the boot drive isn't the first drive in the system. What seems to be happening is that in my case the 320 GB drive is really the second drive on the system (odd that since its in bay 3 but such is life!) but the Mac BIOS is setting up the boot drive as the first drive on the system. I think this is done to make Windows happy but it confuses the heck out of Linux since it ends up booting off the first drive but when Linux is actually running, its now the second drive. Its only grub that is having a problem though so thats easy enough to fix.
To fix it, you need to use "e" to edit the boot params. Reboot the Mac and use Option and with the Windows drive and then when you get to the grub boot loader, press "e" to edit the boot info and then change the line that looks like "root (hd1,2)" to "root (hd0,2)". Once you change this press "b" to boot and it should boot into Kubuntu properly. You now need to edit the /boot/grub/menu.lst file to make the root change above permanent and also to fix the Windows booting. Edit the file and change the "root (hd1,2)" lines to "root (hd0,2)" and also fine the lines in the Windows section that are remapping the drives (should be two lines starting with "map"). Remove them or comment them out. Reboot now and test that you can properly boot into Linux, XP, or Vista.
I think that covers everything I did! The tricky bits were caused by the 8800 GT card and the drive mapping. If you just get a blank screen when booting off the Kubuntu install CD, then at least on my system this was fixed by removing the "slash" option. And likely if I had left the 320 GB drive in bay 1 and just installed the new drives in bay 2/3 then I wouldn't have had to do the grub fixing.