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Did you try disable SIP?

Seems still have lots of unknown about APFS. No sure if the clone can be bootable. Did you try CCC?

I used SuperDuper! (Free) and tested the drive before I converted. It booted fine while still HFS+, it wasn't until I converted to APFS that I received the error so it must be a problem with the latter. I'm thinking an erase and clean install of High Sierra may be necessary?
 
Did you try disable SIP?

Seems still have lots of unknown about APFS. No sure if the clone can be bootable. Did you try CCC?
I used SuperDuper! (Free) and tested the drive before I converted. It booted fine while still HFS+, it wasn't until I converted to APFS that I received the error so it must be a problem with the latter. I'm thinking an erase and clean install of High Sierra may be necessary?

I went ahead and did a clean install from Recovery Mode. Success!
I'm typing this from my APFS volume.
 
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