- boot knoppix cd
- sudo mount /mnt/hdd2
- sudo mount /mnt/sda2
- cd /mnt/hdd2/home
- sudo cp -Rp * /mnt/sda2/
- sudo echo "/dev/sda2 /home auto rw,auto,users,exec 0 2" >> /mnt/hdd2/etc/fstab (or add it with: sudo mcedit /mnt/hdd2/etc/fstab)
- reboot to hd install
- type mount to check that /home is mounted and working and then remove the /home contents from hdd2:
- boot from cd
- sudo mount /mnt/hdd2
- cd /mnt/hdd2
- rm -rf home/*
- reboot to hd install
- done

Knoppix uses grub instead of lilo so no, you don't need to change lilo.conf

- add to /boot/grub/menu.lst:
title Windows
rootnoverify (hd0,0)
makeactive
chainloader +1