First of all, it's great that you have a full bootable backup!
Upgrading Clover on the main disk should be straightforward, but we should upgrade to the latest version, which is 5100. If you decide to try this again (I'm not saying you should do it now), here are some guidelines:
- Ensure that your backup disk is updated and ready for disaster recovery.
- Download the Clover package file (.pkg) from here.
- Run the installer file and select these buttons and options:
View attachment 441186
View attachment 441187
- The installer will mount the EFI partition and it will leave that partition mounted when it finishes.
- Using Finder, examine the files in the updated CLOVER folder.
- You will see a new CLOVER/drivers/UEFIfolder
- Delete all files inside this folder, but not the folder itself.
- You will see the old CLOVER/drivers64UEFI folder as well
- Delete this folder and its contents.
- Download Catalina Fresh Install.zip from the Catalina Mini-Guide.
- Inside the ZIP you'll find a folder called Copy-to-drivers-UEFI.
- Copy all of these files to CLOVER/drivers/UEFI.
- Now add the Boot Argument agdpmod=pikera to your config.plist. This can be done using Clover Configurator:
View attachment 441190
- Save the file and quit Clover Configurator.
- Reboot and check that Mojave still boots up.
- Use the system for a few hours or a day to ensure that it's stable and will boot up repeatedly.
- Then attempt the Catalina in-place upgrade once again.