you can use the dd command to make a perfect image, and then later in linux overwrite the disk with the image...
run as root (DANGER, UNDERSTAND WHAT YOU ARE DOING!)
dd if=/dev/hda1 of=windows.img
to restore, you would do this:
dd if=windows.img of=/dev/hda1
that works for any FS type. I suggest you research this command and learn what it does before entering this command posted here. It will take forever if you have a huge drive (I will copy free space as well, as far as I know)