I just updated my machine from El Capitan to High Sierra using this guide.
I had a few issues, and maybe this will help someone else:
1) I did not convert my SSD to APFS. I have heard some horror stories about doing this, and I didn't see any advantage to it. So, I used the "skip conversion to APFS" section of this guide.
2) I did not update any kexts except for FakeSMC. I used the latest Multibeast to update Clover, and set it to boot from UEFI. Clover wants to change the system definition, so I put it back to one I know works (iMac 12,1)
3) The installer got stuck on a black screen with a white Apple. That issue was solved by checking "FixHeaders" in Clover Configurator. Once that was checked, the installation proceeded with no issues.
4) iCloud didn't work after the update. It had worked before, but something must be more picky in H.S. I had to re-generate a serial number, board serial number, and UUID using this guide:
How to Fix iMessage | tonymacx86.com
After rebooting, I was able to log back into iCloud.
NOTE: if iCloud is not working, and you were using iCloud keychain, most email accounts stop working, and can't be logged into!
After those steps, everything seems to be working correctly.