Copying host setup to a VM

I thought this might be simple, but it appears not to be. I have a nicely working thumb drive that boots and runs quite nicely. I'd like to transfer the images to a VM setup. I've tried copying raw disk files, but then I get into lots of UUID errors, and running GRUB to get a boot sector proves to be "interesting". I'm using the Virtual Machine manager with QEMU/KVM, and creating a qcow image file.

I guess what I'm looking for is a way to take the existing USB stick files and make them into a nice QEMU disk image that will boot as nicely as the original. I tried to do something like this, and gave up after a full day of futzing around (no joy!).

Any ideas?