peppy6582
I would recommend just starting with migrating your Plex setup to Jellyfin. You can get that done in 30 minutes to an hour.
Setting up all of the arr’s takes hours, depending on how intense you want the automations to be (hours to days). I started with Sonarr for TV/Anime direct installed on Windows. Once I knew I liked it and wanted to keep using it, I bought a small form factor PC and installed Ubuntu Server and Docker (which takes a lot longer).
If you can follow guides on the internet, there are tons out there. What OS are you running?
Jellyfin expects movies to be in sub-folders with their movie titles for the best experience. You can have a Star Trek library, but each movie inside of there needs to be in its own folder. For example M:\Star Trek\Star Trek II - Wrath of Kahn\Star Trek II - Wrath of Kahn.mkv
This has always worked the best for me.
I use a reverse proxy (NginxProxyManager). I got so addicted to self hosting I bought a 14 bay server and put UnRaid on it. My job gives me access to decommissioned hard drives, so I filled it up lol. UnRaid makes setting these services up a cakewalk, but it helps to understand Docker to keep it running correctly.
As for video re-encoding, you have Compressarr, tdarr, unmanic, and handbrake mostly. I use handbrake most of the time, but it is manual. I will often times just re-download them in the format that I want. Once you are deeper in the weeds with Sonarr, there are ways to configure it to only download certain formats of video.
Good luck!