Of those items you mention above, I guess only username, password, bootscreen changes and custom drive mappings are actually unique to each individual iso image? The rest (boot options and root password changer) presumably aren't changes made individually on a per cd basis? Those changes can be made to a Knoppix-alike remaster without having to remake the cloop iso, from the config script ammend passwd/shadow/group/fstab (using perhaps echo "">/etc/fstab, or sed). The boot image is also held outside of the cloop so you can create it by whatever means you want, and drop it into the new image. So all you have to do to create the image is a plain mkiso which takes 100th/1000th the time of making the cloop image.