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clone that puppy
Various folders have different permissions, and the symbolic links may not be created with a regular file copy. There are ways to maintain permissions and symlink structure, but not in a simple copy. Plus there's the boot sector and related files as mentioned above.
I also said mbr (master boot record) which is not copied when you copy just the partition.
Also another caveat - the new drive might be using different sized 'blocks'. When I run fdisk -l from a Linux distribution it will sometimes state that 'partition 0 does not end on cylinder boundary'. This causes performance issues, because adjacent locations have to be read to obtain all original data.
Sadly cloning is also kind of a hack. The best tool here would be the Windows installer.
fsutil behavior set disabledeletenotify 0