It may be useful to go back to an empty 1TB drive, use disc utility to erase and partition it, do a minimum 3 pass erase which is going to take hours but will ensure there is no carry over from the faulty install. Ensure that you select the Mac OS Extended (Journaled) setting and in the options select GUID partition table, when you get to partitioning time.
Sounds like your clone may not have been set right. There should be an option for creating a bootable clone somewhere in the preferences, not all clones are. Super duper is not the cloning programme I use so you’ll need to read the manual to see what is required.
From bens comment above it should be possible to re-size the partition in disk utility without wiping the data. It’s a drag the slider job and hit apply.