To avoid any extra complications, I have switched from cloop to squashfs, and by stripping down minirt init, I can get /UNIONFS correctly mounted. But there is still no way I can get next step started: With manual chroot into /UNIONFS, I can start /sbin/init, but it won't run correctly, it seems. So there must be something with busybox and full 64-bits mounting. Different versions of 64-bits busybox don't help, and compiling latest version (1.1 from source only makes things worse for me. The last resort, as I see it now, is to include mount and bash, with necessary libraries, in minirt. This is by no means far-fetched, as the two functioning 64-bits initrds I have checked, Debian 6.0.1 and Kanotix 2011/5, both include a lot of system programs, while Knoppix only has busybox and ntfs-3g. I have compiled and started using kernel 2.6.39.2-64, but it doesn't help much, it seems. (Nor did a freshly compiled cloop from Debian-Knoppix, before I turned to squashfs.)

As far as I can see, there is no need for a special init for 64-bits, just other programs. But it may be a small challenge to modify init to include squashfs handling in an optimal way.

Knoppix "pure" 64 bits full HD install works well, including qemu, which I use for testing images and minirt.gz versions. So remastering from this version should be possible.