I would NOT clone from partition to partition in this scenario, since you cannot simply replace the internal harddrive with the external harddrive and boot from that.
Instead I would "image" the partitions to image files on a large (single) NTFS partition on the external harddrive. Any good imaging tool should be able to do that while saving only the active/used data on the source partitions and while compressing the data to some degree.
Tools that I have used which can do this include: Acronis TrueImage (commercial), Macrium Reflect (commercial or free), Clonezilla (free).
The one thing you need to look out for is, that the recovery tool should be able to boot from CD/DVD or USB and be able to see yor internal and external drives on that computer; even those tools that can run from within Windows cannot necessarily "see" all your drives when booted from recovery media - this depends on the software, your hardware, your BIOS settings and probably phases of the moon.