It's a nice safe feeling to be doing all the exploiting and experimenting on a new drive and have the stock-drive tugged away in case something should go wrong.
I can recommend cloning your drive using linux. Doesn't have to be a speciel linux with fatx support or anything. All that's needed is :
1) get your xbox eeprom
2) Hotswap stock xbox drive (or unlock with passwd from evox/ConfigMagic)
3) Attach stock xbox HD and new HD to your PC (assuming xbox HD primary master and new drive primary slave)
4) boot a linux distro. Could be xlinux booted from cdrom-drive.
5) Be very sure the stock xbox HD is /dev/hda and the new drive is /dev/hdb. Running
Will list the drives attached and you should be able to tell which is which.
Clone the HD.
| dd if=/dev/hda of=/dev/hdb bs=512k|
6) Use liveinfo and your xbox eeprom to generate passwd for the new drive.
7) Lock it with unlockx.