Help with restoring backups

My YunoHost server

Hardware: Raspberry Pi 4
YunoHost version: 11.2.9.1
I have access to my server : Through SSH | through the webadmin
Are you in a special context or did you perform some particular tweaking on your YunoHost instance ? : yes, some custom config

Description of my issue

I’ve built up significant “config crust” over the years so I want t migrate to a new instance. I backed everything up, made note of all my custom config things lie fstab and my swap settings and started copying everything over. The first issue I’ve run into is trying to restore the *arr apps, and Nextcloud:

2024-02-09 17:13:55,902: WARNING - setfacl: /home/yunohost.multimedia/<every single user>/Share/Torrents: No such file or directory

I suppose I could just manually make the folders but then I wouldn’t know what to do for permissions etc. Is making the folders not part of the restore script? It must have been part of the install script, no?

Next is a similar issue with Transmission:

2024-02-09 17:23:41,011: WARNING - chown: cannot access '/home/yunohost.app/transmission/progress': No such file or directory

EDIT:

I’m seeing a common theme here. Synapse is doing the same:

2024-02-09 18:48:22,774: WARNING - ../settings/scripts/_common.sh: /opt/yunohost/matrix-synapse/bin/pip3: /opt/yunohost/matrix-synapse/bin/python3: bad interpreter: No such file or directory