1) If it was the same USB, then there's little likelihood that's what the storage crash is about.

2) Strange. Makes you wonder if there's areas of the flash memory that are defective and getting masked by the SSD's scavenger routines built into its firmware. (likely the only thing that would tell you the true state of the drive would be to get something like Hiren's boot CD and run the Seagate diagnostic tools on it).
http://www.hirensbootcd.org if you're interested. Just suggesting that's what it sounds like....with things seeming to gradually get more stable.
If apps aren't compatible with Sierra, it likely won't matter which approach you take - TM restore, then Sierra upgrade overtop or a clean Sierra install, then use migration assistant with the original drive (presumably you have a USB enclosure you've put that one into?).
If I were you, I'd remake the Sierra patched installer, to rule it out (but, if you had the old one kicking around, I would have used that one, as it worked)

It's not the version of the tool, it's that people have had issues with their USB drives having glitches.
Me, I'd still want to run Samsung's diags on that SSD to make sure as well. Being a brand new drive, if there's any glitches in it, I'd be returning it pretty quick (but you need the diags to tell you that).