Success! I updated the Lilu kexts this morning, so those were up to date already. The Updates notification popped up, so I backed up using CCC, then copied over my EFI. Then I went to About This Mac and chose update. The update started downloading and then when finish, the system restarted.
It went through a "soft restart" ie., the screen went to the white logo on black without going through POST/BIOS. The progress bar went to about 10%, then the system restarted.
It went through POST/BIOS then into Clover. I chose Preboot, then it progressed to the white logo on black. After a few minutes, the system restarted.
It went through POST/BIOS then into Clover. I chose FileVault, then it finished. This was the longest part. Finally, I emerged to the login screen. I logged in, then did a manually restart.
Done!
All in all, maybe 15-20 min. I was on a conference call, and it completed before the end of the call...