I've never had any software or drivers for external drives installed. I use a Lacie external connected via Firewire 800. I had tried unplugging everything except the keyboard, uninstalling or disabling a lot of 3rd party apps and utilities and pref panes, trashing countless prefs. None of it made a difference. The Sys Prefs freezes diminished slightly, but the finder quirks and no logout/restart/shut-down issue remained — especially after an hour or so of processor-intensive work, like running several Adobe CC apps simultaneously. And this was happening on my desktop and laptop Macs. So, IMHO, it looks like a possible memory leak problem?
Since restoring 10.8.5, I have had zero problems and 100% uptime. If you're lucky, your measures will, over time, prove to have worked for you. But — and I don't mean to rain on your parade — I wouldn't be shocked if you saw an encore performance of these problems in the near future.
BTW, since I don't use my MBP for graphics work very often, I'm leaving Mavericks on that machine as a "crash dummy". I'll see if 10.9.1 or .2 make a difference, and when I can do the heavy lifting on that machine, I'll upgrade my Mini again. My clients pay me to do their advertising, not to reboot my computer a half dozen times a day. 😉