After restart, all user settings are gone and reset to defaults

Hi after waking up my iMac from sleep today, it appeared something had gone wrong (apps not responding…notification that my external drives had "not been ejected correctly" etc). I restarted. After restart, and logging back in to my regular user account, all user settings were missing and reset to factory defaults: Desktop reset to the "wave", Dock reset, Download folder missing (grey question mark), Dropbox unable to connect, Safari bookmarks missing (but still on my iPhone-- so it's a local iMac problem, not an issue with iCloud), small things like mouse scrolling prefs reset etc.
Basically all of my user preferences are missing. I've seen a number of threads about how to fix some of these items individually, but seems like there is a single corrupt preference file somewhere maybe?
I've repaired permissions a few times (there were a lot), and restarted but nothing has fixed it yet.
I had been logged out of iCloud, but once I logged back in, my Mail came back (just my me.com account-- still missing my Gmail, will need to reset I guess), along with Calendar and Contacts-- those are ok.
I keep all my files on an external LaCie RAID, and that all appears to be fine. Folders all intact etc.
Suggestions?
Thanks for your help!

Try booting into the Safe Mode using your normal account.  Disconnect all peripherals except those needed for the test. Shut down the computer and then power it back up after waiting 10 seconds. Immediately after hearing the startup chime, hold down the shift key and continue to hold it until the gray Apple icon and a progress bar appear and again when you log in. The boot up is significantly slower than normal. This will reset some caches, forces a directory check, and disables all startup and login items, among other things. When you reboot normally, the initial reboot may be slower than normal. If the system operates normally, there may be 3rd party applications which are causing a problem. Try deleting/disabling the third party applications after a restart by using the application un-installer. For each disable/delete, you will need to restart if you don’t do them all at once.
Safe Mode - Mavericks
Safe Mode - About
Try running this program when in your old account and then copy and paste the output in a reply. The program was created by Etresoft, a frequent contributor.  Please use copy and paste as screen shots can be hard to read.
Etrecheck – System Information

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