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#11
Once you cloned the HD the fact C has no System flag tells you that you still need to repair or write the System boot files to it.
To do this unplug the other HD, make sure the clone is set first to boot in BIOS setup, then run Startup Repair - Run up to 3 Separate Times until C holds the System Active flag.
Now you can plug back in the other HD, boot it if needed by tapping the one-time BIOS Boot Menu key at boot. If you want to use it for storage, wipe it with Diskpart Clean Command then partition it in Disk Mgmt.