Fed up with trying to find the solution and after 500+ people said "I have this problem too"....
I did this:
Make a Yosemite Boot Install USB ThumbDrive. (good to have one around anyway)
Open ONYX and make all folders an files visible. <-----very important to copy everything including all the hidden system stuff and hidden library stuff.
It ensures that when you bring it back..most of your settings are there will save you time.
Copy EVERYTHING - Do NOT USE TIME MACHINE...when you come back from Time Machine it will bring El Capitan back.
---You can use CarbonCloner, SuperDuper or just drag n drop folder by folder to a backup drive including all those hidden files off main drive. (some of these you can't copy...that's ok) COPY APPLICATIONS, SYSTEM Folder and all LIBRARIES including your USER LIBRARY. --- Some files are fussy....you might have to GET INFO on some of them, unlock them and give yourself privileges.
- VERIFY that folder sizes are exactly or close to a match from backup from your MAIN HD...before you...
- Boot up with Yosemite USB Thumbdrive (COMMAND-R)....and use Disk Utility to Erase your MAIN HD.
- Quit Disk Utility and choose INSTALL OS
- INSTALL Yosemite on it.
- Boot up
- Re setup your settings...by doing the following:
Copy BACK OVER only things you NEED.....except SYSTEM stuff. There might be one or two things in there that you might want to bring back...but UNLESS you know what it is..like Hamachi/Logmein)...don't...and.. most likely NO)
Copy over ONLY WHAT YOU NEED back from the HD/LIBRARY. Stuff related to Pro Apps, Adobe, Application Support folders (just ONLY what you need), Preferences like Firefox Mozilla profiles..etc. ONLY WHAT YOU NEED.
Don't open anything till you have copied over those preferences..etc.
REBOOT after copying all that stuff back.
FRESH!!! yyyeeaaahhhhhhhhh!
I started this all by back up and did the erase and fresh install before bed.....the next day when I got home..took me about an hour or two to get all the stuff I needed back.
NOTE: I do run Server and bringing the Server folder back to Library worked! (Everything except my users and SSL certificate I had to reissue) - Great!
I was actually surprised with how fast it took me to get everything back.
I'm back to lighting fast computing on a 2010 Mac Mini. Everything is running faster.....NO SPINNING WHEEL.
And one more thing....DO NOT UPGRADE to El Capitan until you hear otherwise that they have fixed this.