I've had an almost exact experience on my Mid-1012 Mac Pro.
But I have multiple HD's in it and the ability to boot off whatever system I have on the HD of choice.
So...When El Capitan would boot after initial install I tried everything with SApple Tech;s Help.
Nothing worked.
I could clean install and get it running, but as soon as I migrated data/files/progras, it would hang on restart.
I finally re-intialized the drive and reinstalled Yosemite and spent the next 4 days migrating data/files/programs back onto it.
It's running fine, and until there;s a few versions of El Capitan working I'm sticking with my stable 10.10.5 Yosemite booting off a Crucial SSD.
Here's another little "Apple Trap".
Update to El Capitan.
Run Photos.
It'll request to migrate your photo library.
IF it runs, it will import them.
When the entire OSX Crashes, and you try to re-run your Yosemite Photos, it'll say the photo file only works with a newer version, and YOUR YOSEMITE PHOTO LIBRARY CAN'T BE READ ANYMORE.
If you don't have a clean backup of your Yosemite Photos File saved, you could lose everything.
BACKUP CRITICAL FILES BEFORE UPDATING TO El CAPITAN and then make another backup somewhere else to be safe....BEFORE UPDATING OR RUNNING 10.10.11
Don't ask me how I know. I do keep multiple back-ups in my Mac Pro, fortunately.