I'm assuming that both drives are connected via a USB interface.
Regardless of how you cut it.....that's going to be painfully slow in hours or even days. Any backup program run from within Windows should be able to see both drives and perform the Cloning operation.
I recently did something similar using two SATA II drives, but they were both connected to the motherboard's SATA ports for both speed and efficiency.
* USB is just too slow for operations like that.
I used Ghost 11.5 (Ghost32.exe) run from within Windows XP. The whole job worked perfectly.