So you've already got Linux experience? Personally, I would boot some Linux distro from a USB stick or Live CD - Puppy Linux for example is great (and btw super handy if installed on a USB stick).
And then simply use the powerful dd command to clone:
dd if=<HDD device you want to clone, for example /dev/sda> of=<HDD device you want to copy to, for example /dev/sdb> bs=1M







