Sorry, I should have instructed you to re-install Clover on your macOS drive before replacing the Clover folder, as you were using an older version on your main drive, compared to the USB.
You would need to follow the steps shown in the earlier post, but make sure you selected your main macOS drive and not the USB. Everything else would be the same, i.e. select the top two customisation entries in the list, leave the other customisation options alone. Then when the installation has completed replace the CLOVER folder on the main macOS drives EFI Partition, which would be mounted on your desktop, with the CLOVER 3 folder.
No idea, other than a clash with the old Clover version, as to why you wouldn't see your Mojave drives icon on the Clover boot screen. I only made the three changes to the config.plist as stated above.