I'm still having problems now with compiling a new kernel working with minirt.gz

I have a HD install of knoppix which is now running with kernel 2.6.27-4 and boots ok.
I created an initial ramdisk with mkinitramfs -o initrd.img-2.6.27-4 (to comply with naming system)

I have my remastered knoppix on /media/hda14/knx (as remastering instructions)

I can copy kernel, /lib/modules across but my problem is how do I create a new minirt.gz?

I change into /meida/hda14/knx/master/boot/isolinux
unzip existing minirt gunzip minirt.gz
mount it ( mkdir tmp && mount -t ext2 -o loop minirt ./tmp)
If I change into the tmp directory I can see the expanded miniroot section with modules directory etc

Do i now just copy aufs.ko and cloop.ko from my 2.6.27.4 kernel into the minirt module folder or am I
missing a few steps?
Thanks in advance.