Ok I've fixed Plex! :D The trouble is, I'm not 100% sure what I did... General idea below (probably lots of unneccessary steps):
After removing Plex and its jail, I reinstalled it in the web GUI.
I started Plex using service plexmediaserver start (or possibly onestart; whichever works)
I checked it was running with service plexmediaserver status
Stopped with service plexmediaserver stop (or possibly onestop)
Then went ls -l /var/run to check my permissions
There are several lines listed, but the two in question are:
drwxr-xr-x 2 plex wheel (date/time) plex
-rw-rw-rw- 1 root wheel (date/time) plexmediaserver_fcgi_server.pid
Changed permissions with chown -R media:media /var/run/plex (I knew this wasn't the correct UN/PW but wanted to try it anyway)
Changed permissions with chown -R media:media /var/run/plexmediaserver_fcgi_server.pid
(By the way, this is all per this post: https://forums.freenas.org/index.php?threads/plex-plugin-works-but-won't-start.38867/
Then I read Joshua's comment about not changing the fcgi line
I checked in the GUI the relevant permissions on my movies folder which is root:media
Changed permissions with chown -R root:media /var/run/plex
ls -l /var/run now shows:
drwxr-xr-x 2 root media (date/time) plex
-rw-rw-rw- 1 media media (date/time) plexmediaserver_fcgi_server.pid
Then from root@FreeNAS I ran this command to restore my config (see my post above about this):
cp -iprv "/root/backups/plexdata/Plex Media Server/Preferences.xml" "/mnt/media/plexmediaserver_1/var/db/plexdata/Plex Media Server/"
From there I couldn't get the server to start. Interestingly enough, browsing to <ip>:32400 worked, however it didn't show this server, only my other Plex server.
Changed permissions BACK with chown -R root:wheel /var/run/plexmediaserver_fcgi_server.pid
Still couldn't get the service to start
***Then via the GUI, I restarted the jail*** (key point)
Typed service plexmediaserver status, discovered service is running
Tried browsing to server and it now works!
Sadly, my settings haven't copied correctly (eg media locations and watch history) but at least it's working now. Incidently, now CP isn't showing its logo and is showing OFF in the GUI, but it appears to be working. Unsure if it has write permissions as of yet - I'll leave that for another day. Transmission is still complaining about write permissions too; but I think I've done enough for one day.
TO ADD: I just refreshed my browser a couple of times and now all three plugins are showing down the left. CP sometimes says ON, sometimes it says OFF. CP logo also decides to appear or disappear (both down left and under Plugins) when refreshing browser. Odd. Status with SSH shows running. Will continue to observe.
EDIT: I also just noticed Plex was getting playback errors when trying to play media (my previous version was probably outdated). Easy fix - just click on the three dots next to your media folder and hit Analyse. This gets Plex to download the relevant codecs for the media.
Thanks for everyone who has helped me with this. Hopefully my info above can help others.