... making clones with Carbon Copy Cloner, which I worry is not fully up to speed with Yosemite yet.
I don't know exactly what made you question CCC's compatibility with Yosemite, but
Bombich claims
the current version (4.0.2) is 'ready to rumble' with Mac OS X 10.8 and up.
I upgraded Mavericks to Yosemite, then ran CCC. So, I wasn't using the very latest version. That must have caused my problems. Starting from stratch, then using the lastest CCC added a step: cloning an invisible Recovery HD before starting the standard backup. I love a learning curve.
Also, I noticed fonts are causing me grief:
I like to take all but the necessary system fonts out of play and move them to a new folder, then manage them with Suitcase, a la Kurt Lang.
There is some sort of System protection that makes moving or even copying fonts a challenge, throwing up a system error dialogue even when booted from a SL partition.
I've been flailing a bit, so can't describe exactly how I've approached this so far, except to say that it always worked with every system up to Mavericks.
Also, I've just noticed that Suitcase has still yet to release a Yosemite-compatible update. Suitcase Fusion 4 and 5 seem to work, but aren't officially compatible.
