Always no matter what, have a clone or three - clean, working image, last version before OS X 1.2.3 that you are about to install.
It is about INSTALLING OS X, not updating once you have it - though updates and security updates are known to be monkey wrenches too at times.
Never remove safety net, no matter how safe it seems.
Use a clone to run DU and repair the drive, the drive partition, it handles both (partition integrity was new to Lion), AND to invoke TRIM command when repairing (which won't happen in recovery partition mode of DU).
CCC does a smart update. You don't worry about applying updates to those, and in fact wait a few days before applying updates sometimes, or just make sure the clone is up to date so you can boot from and do a restore if needed. A system restore image is only as good as knowing it will work in an emergency should one arise.
Like to see people break ground on new projects and how to get more out of their systems. The 5,1 does not have the limitations or issues that even the 4,1 exhibited let alone even more for the Early '08 3,1s.
One good SSD alone should / would / make more improvement in performance for low investment than any I have seen. If you have the Tempo Pro card and 2 x 250GB 840's that is about $600 investment - throw in another system SSD and use the Tempo for scratch and/or Aperture and insure you have "more than enough" RAM and your workflow should be smooth. Even wtih that, which I call "best practices" the nMP 6.1 makes Aperture etc even smoother as everything is optimized better and the 1200MB/sec SSD and 4-channel 1866 DDR3 makes graphics smoother and respond instantly to your touch (sports car handling vs your sedan?)
After doing a lot of installs, upgrades, Migration Assistant; and then on a 2-4 week basis boot from another volume to run DU Repair.
OS X alone without the cache used and other things on the boot drive really only takes 40-160GB and makes it easy to create a DU sparse disk image for CCC to update and restore from and that can be kept anywhere. And have a small 200GB emergency maintenance boot volume that you can add to and create on any volume you have handy, shrink and add to that 2TB media drive or TimeMachine drive volume.
I would just set aside half an hour weekly or as needed to clone your system. Than clone again before you apply anything, system update or update to applications or new applications.
With all your personal data and media and projects not on the system you don't need a RAID0 array to hold as much data, no need for the added complexity or using two SSD devices, easier to maintain and restore. There is even a small added overhead to any RAID. With an 840 EVO 500GB just above $300 it makes a lot of sense to use those, and almost too big for a system drive. Fine if the system drive is not just OS and applications but media and stuff don't need to be there. Again, Aperture/Lightroom and other uses, yes and with t he new Mac Pro people are putting and using it for multiple purposes and uses that they would not have wtih the 2012 5,1 and earlier. But it is so fast it makes sense - and Thunderbolt 2 external storage has added more costs to storage.
Kind of got long winded, hope it proves helpful. And not confusing but may raise more questions and ideas.