I was going to say just use Clonezilla and do a disk to disk clone. Long as you have the space available it's fine. I use it for my Linux boxes, it'll copy MBR sectors too so you shouldn't have any issues with bootloaders.
As for backups,
Rsync is the way to go, there is a windows clone cwrsync. Syntax may be different but you can clone to local or remote disks with it.
Under Linux you can use the --delete flag and it'll wipe extraneous files from the target disk (the one you copy to) if files don't match the source.
It's slow on initial copying but then only changes represent a delay upon backup, only transfers data that is actually needed to.
https://www.itefix.no/i2/cwrsync