How to create at time of new install

I can suggest a couple improvements, but this is the essential process.

We could suggest you consider:
get an SSD for booting. Put it in the lower DVD tray. This will make your system much faster also.
If you already have your system set up as you like, use SuperDuper to clone your internal boot volume to an external disk or as a disk image.
replace all the disks, and create the volumes as desired.
Run SuperDuper to clone your system back to the Mac Pro.
Run SoftRAID and "rebuild boot cache" to make that system bootable.

Thanks for the response.

I did consider the SSD option, however, not that bothered about the increase in programmes loading - after all this is OS X.

I need the SSD I am getting for my camera, which is why I need to upgrade the discs in my Bigmac, which is why I need.. :)

Oh, but thanks for the idea - I can convert the lower DVD to a caddy for the SSD from the camera - that will save so much time transferring via SATA than USB / thanks!

Well, I've got to the last stage, booting the installed copy of OS X on the raid, and nothing.
And it's nothing as I have a non Apple GPU, so I only get a screen once loaded.

Have unplugged the fw disks and am trying to boot again, failing that I guess I have to remove two disks physically and see if it will then boot from fw.

Most effort I've spent on it since I got it in 2008 :)

Did you clone the system, or use an OS X installer image?

If a clone, boot from a similar OS (like on a thumbdrive) , run SoftRAID and "rebuild boot cache" on the SoftRAID volume

I installed the same way that I did for the bootable copy on the fw drive.
Ran the installer downloaded from the App Store.

It did load once, installed the updated driver, and now isn't restarting - my bad, only just remembered that bit.

That's the problem, as I have a non Apple firmware video card, I don't get to choose a startup disk by using the alt key. I have to choose in sys prefs and restart - hence thinking I need to remove two discs physically, so it forces a boot from the fw drive' don't even have a MacBook around to use target mode. And I can't VNC to it from my iPad.

the installer should have left it bootable.

If you connect the drives after boot (assuming you can startup as you described), then run SotRAID, select this volume and "rebuild boot cache", does that fix this issue?

Can I plug in the internal discs on a Mac Pro 3.1 whilsts it's running?
I thought it had to be turned off.

You had mentioned FireWire, so I was assuming you could connect the disks via FireWire.

I think on this specific machine you need a different strategy.
Purchase a reasonable price/sized SSD. Put it in the lower DVD tray. Pre set it up for booting (in Apple format) and use that for booting this machine. Use your mirrors (RAID volumes) for data only. It will be simpler in a setup where you effectively don't have keybaord/monitor access at startup.

Yep. Came to the same conclusion.
Problem is I now can't boot off FireWire, plus if the physical discs are in it just reboots.

Was going to try booting with one physical in at a time and destroy the data, if I could...

Put your machine into Target mode. Connect it to another computer. Option boot FROM the Mac Pro. Then set startup. (while you are at it, you can try to rebuild the boot cache)