> I do that routinely. Boot from a liveUSB, rsync data from the main system, fix the bootloader and a couple of configs like /etc/fstab. Works like a charm every time.

Just be careful if you intend to keep the old system running. You probably don't want to clone /etc/machine-id and similar (see: the problems that come with exactly cloning VMs). But of course, if the old system is being destroyed, then no worries.