Glad to see all is well.
On a final note, in general Windows can get a bit "confused" when there's another version of itself visible on another drive (or partition). Not that this is the cause of this particular problem but still.

If it were me I'd do the cloning of the disk using Macrium's Rescue environment. When that's done I'd go into bios, test boot the cloned disk and when all is well I'd just disable that drive in bios.
That's how I did it months ago.
Nowadays I gained so much confidence in Macrium that I just let it make system images which I keep on an external USB drive.
At the rate MS is updating their latest brainchild you can easily find yourself doing more backups than anything else nowadays........
Macrium's help file which you can either consult online or download is worth a read.
After that pick the policy that suits you best.

I absolutely second NavyLCDR's opinion. Not only is it better, it's also more complete and quite a bit faster too.