I first moved the initrd.img and vmlinuz from the /live folder on my usb to my desktop (for backup).From within my non-live dist, with my usb inserted:
The vmlinuz-4.9.0-kali4-amd64 was already available. I was able to simply create a initrd.img file (it was missing) using update-initramfs, and moving this to the live folder manually from my non-live linux dist: /usr/sbin/-tools -c -k 4.9.0-kali4-amd64 Instead of messing with mounting/unmounting etc.
Due to a bug in either the way my live system was installed or the way live-tools handles the mounted partition, live-update-initramfs does not work in this particular case, as it looks to /lib/live/mount/medium/ as the root of the usb live device, though this was not the mountpoint (and there are 3 partitions needed from the usb device).
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