Well, my system is still screwed up. As I said above, everything was working fine. Machine could shutdown and start up just fine. I did a fresh backup on CCC and on TM and then decided to do the latest update to El Capitan. During that update, the machine would not do what I think is the final boot to complete the upgrade. The progress bar was frozen at about the 60-70% point. Left it there for over an hour, just in case. Finally shut it down with the power. Powered back up and machine wouldn't boot.
Back to square one.
Tried to start the machine with CCC that was supposed to be a bootable drive, but that wouldn't work.
Reloaded El Capitan with the bootable thumb drive loader and reinstalled El Capitan.
All programs and other data intact. Tried a shutdown and start and the progress bar didn't budge. Disk wouldn't start.
Restarted the machine with Com + R.
Since I didn't see a way to start CCC, I'm now restoring with the TM backup I had just made. That's going to take a couple hours.
Am I correct in my thinking that I can not Clone the internal drive from CCC if the computer booted from the internal drive? For instance, could I have reloaded the Op Sys with the thumb drive, then just use CCC to clone to the hard drive?
Also, do you guys think my HD may be dying? Everything worked fine while on Yosemite, and once booted up on El Capitan, everything had worked until you do a Sys update.
For now, when I get my system back to where it was before I tried that update, I'm done with System Updates until the next Op System comes out.