I would do something like

sudo rsync -avx --exclude=".gvfs" / /path/to/backup/folder/

(The -x option makes it ignore other filesystems, which makes it work even on a running system, which is great for backups!) You will want to do this step for each partition you decide to back up.

Once you have the partitions the way you want and windows installed, I would boot a Ubuntu LiveCD/USB. Then mount the new partition and backup partition and run something like

sudo rsync -avx --exclude=".gvfs" /path/to/backup/folder/ /path/to/new/mounted/partition/

You will want to do this step for each partition you want to restore.

Run sudo blkid to get the uuid of each of the new partitions. Then run

gksudo gedit /path/to/new/mounted/partition/etc/fstab

and change the UUIDs and then save the file.

Then I would follow the instructions on Grub2 Reinstalling from LiveCD in the "Method 3-Chroot" section to install Grub and let it detect the new disk layout.