Okay, thank you for the quick reply.
You mean the configuration file of FreeNAS itself right, not my plugins?
And my ZFS data shares will be safe as well I guess, right?
That's correct. Make sure to back up your configuration file from the GUI: System ->Settings->General->Save Config
Your jail and ZFS pool are stored on the hard drives and are separate from the OS (at least it should be), so they will stay intact as long as you restore your zpool through the config file after you upgrade (System->Settings->General->Upload Config).
From my experience, the upgrade process went very smoothly except for the jail migration.
You have to log on as root to the NAS and execute /root/migrate_pluginjail.sh -D to migrate 8.3 jail to 9.1 jail.
It didn't go that smoothly for me as it was not able to auto-mount the jail volumes and I had to fix that manually, YMMV. Also, the storage page on the main GUI page is bugged and you have to use the add/edit from the tree on the left.
One thing you may also like to know is my TransmissionBT plugin ceased being a plugin anymore (no longer shows up under plugins page). It's not a big deal cause it still runs normally in the jail, but you just have to start/stop it through the shell now instead of the plugins GUI page.
Good luck!