I managed to fix my MacPro4,1 with RAID array ... It was fairly contrived and took me a weekend, but I'm really happy with El Capitan now.
Luckily I had access to another Mac to build myself a USB key containing the El Capitan installer.
My symptoms were pretty horrendous: Wouldn't boot into Restore, Single User or Safe Mode off the internal El Capitan install.
Set up is MacPro4,1 with 4x1TB AppleRAID configured striped mirrored-pairs (RAID1+0??)
[1] With access to another Mac I downloaded the Installer and built a bootable USB key
[2] Insert the USB key in MacPro4,1
[3] Reboot the MacPro4,1 holding the Option key and chose the USB key to boot
Before I did anything else - I took the paranoid approach of duplicating my Macintosh HD onto another disk.
Yes - I've got my TImeMachine backup - but I'm paranoid, so after searching around on how to use Terminal.
My internal volume was using 684 GB of a 2TB AppleRAID.
After multiple attempts, I realized I had to wipe the internal disk and rebuild the RAID array. I decided to take the opportunity to build a CoreStorage logical volume for a Fusion drive with a 500 GB SSD front-ending a 4x1TB AppleRAID array. That way I could have an OS Recovery and a faster experience. You don't need to do this, but I concluded that since I was erasing the disk and recovering - why not make the machine a lot faster.
[4] I took the gutsy and terrifying step of using Disk Utility (which I hate on El Capitan) to erase the internal disk (TimeMachine = check, independent duplicate = check)
I then used Terminal to destroy and rebuild my AppleRAID, and then construct a CoreStorage volume across the SSD and AppleRAID.
Took some Google searching to find out how to "Build your own Fusion drive" and "AppleRAID and CoreStorage". Useful articles ...
http://forums.macrumors.com/threads/advanced-core-storage.1566527/
http://blog.fosketts.net/2011/08/05/undocumented-corestorage-commands/
http://www.cnet.com/how-to/how-to-make-a-custom-corestorage-drive-in-os-x/
[5] Once I'd rebuilt my RAID and CoreStorage Volume ... I had a blank "Macintosh HD" disk
[6] Reboot again on the USB key and then Install the OS.
[7] Once the OS had installed, I then used the migration assistant to chose to migrate from my TimeMachine - do a custom migrate to get Users, Applications and Computer Settings.
[8] Once restarted, logged in as each user and confirmed that Applications, esp Mail, iCloud etc were set up correctly for everyone
This last step took a little while, I had to find Microsoft Product Keys and reactivate my version of Office.
I've still got a couple of applications that really dislike SIP changes, so I need to work on those.
That said, El Capitan is pretty good.
[9] Reconfigured TimeMachine and ran a full backup
[10] Restarted the AppleTVs around the house and checked that iPads etc can access iTunes.
Some minor stuff to fix this coming weekend ... but I realized that if I make sure I have:
(a) up to date Time Machine backup
(b) OS Recovery partition AND USB key / drive with the latest installer - being able to boot independently is crucial for a complex machine like mine
(c) Independent access to Google / Apple Forums so I can find the right Terminal commands
(d) Access to product keys
...
(e) Patience ... I've got 16,000+ images and 1000's of iTunes tracks, Podcasts, iPad Apps ...
The approach of Clean Install and Migration seems to be the approach I'll adopt again.
It cleaned out all the kexts that had been lurking in there since Lion, Mavericks, Yosemite ... etc
Side benefits:
+ My machine is a lot faster with the homebuilt Fusion drive I built in the process (good story about how to build that from SSD + 4x1TB - all internal)
+ I've decided to upgrade the RAM in the machine (32 GB in 4x8GB)
+ Machine has been stable and up for the last week or so.