@kcdobe,
Did you follow the
How To Install OS X Yosemite Using Clover guide when you switched to the Clover boot loader? If not, take a look at the guide as it should answer your question on the /extra folder, etc.
I
always create a new UniBeast Installation USB Thumb drive. Because if "fruitcake" happens, you'll need to boot with the thumb drive.
You can install High Sierra either way - on top of your Yosemite build or a fresh install on another drive. If you do a fresh install, the installation will ask you if you want to migration your apps and accounts from the other drive; don't check "Other Files" (IIRC that's the name). Either way you'll need to run MultiBeast. However, given you're jumping from Yosemite, I recommend a fresh install then migrate your apps and accounts.
Good Luck!