Alright, I've made some progress.
I managed to restore my partition table with sudo gpart -W /dev/sdb /dev/sdb
from the Live CD on the original USB, and to clone it (properly this time) to my HDD with clonezilla. GRUB was still not working, so I followed the instructions from this topic to reinstall GRUB. While chrooted into my HDD I confirmed that the system contained my files, and that they were not corrupted.
Now, GRUB works and the system seems to start up, but while booting up, it just shows [FAILED] Failed to start Samba NMB Demon
, which is weird because I recall I had uninstalled that.
Would you guys have an idea of what I did wrong?