You can just copy the entire contents of your /config folder (including the hidden .storage folder) to your new system. You would then only have to install and set up any addons you use. Copying the configs from these to a text file before updating would make this easier.
You should also post in the samba backup topic. The dev responds to issues there.
https://community.home-assistant.io/t/samba-backup-create-and-store-backups-on-a-samba-share/199471