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I know that I was trying to not blow away an entire 2 TB drive for a 500Gig backup.
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What does that comment mean? What *exactly* did you do? Why are you worried about the size of the disk and partitions? As I've said several times you can change all that later. Please stop asking about partitions and partition sizes and either do what is suggested or tell us *exactly* what you have done. What exactly is on that clone drive now? Can you post a screenshot of Disk Utility showing all the drive containers/partitions.
What I wanted you to do is get a APFS partition on the drive. If you ended up with HFS+ it's no big deal. I am fully aware of all the different recommendations for what filesystems to use for what.
No Applications. What *exactly* does that mean? You Have to explain stuff to us clearly.
What exact Applications do not appear and how exactly do they not appear. Where/how are you looking at stuff? Are you looking in /Applications in the Finder? Using Terminal? Talking about applications appearing in the Dock? On the desktop?
In Terminal.app (do you have Terminal.app?) while booted from the clone type the following commands and paste the output here.
mount
ls -l /Application
Could you log in OK as the same user when booted off the clone drive as when booted off the internal drive? Or did it look like you were doing a clean macOS install setup?