I have Jellyfin installed as an application on my TrueNAS scale server.

I have tried for months, off and on, to get it setup but Jellyfin can never list my media which is hosted on the same server.

Can someone point me in the right direction?

Is your folder/file/Library structure setup for Jellyfin?

First Movies and Shows need to be in separate libraries
Shows require a Season # folder even if there is only 1 season.
File names need need Season # and Episode #

For example
My Folder structure is setup something like this
TV Shows\Band of Brothers\Season 1
Files:
Band Of Brothers S1E01
Band Of Brothers S1E02
ect

In Jellyfin I have a Show Library that includes everything in folder TV shows

For Metadata I use TinyMediaManager to create nfo files which Jellyfin can use, just turn off all online scrapers in the library settings. I found that scrapping within Jellyfin is prone to error because there can be differences between in data between "aired order, DVD order" ect and sometimes even the online Metadata service like TVDB aren't even 100% correct and manual clean up is needed  DVD order may be correct for the episodes but there's no DVD Order metadata for the extras, which fall under Aired order.

My media folder is setup as:

Movies/list all movies
TV shows/TVshow/S1/list all shows

File names are S1E1 etc.

That setup works great with Plex....

https://jellyfin.org/docs/general/server/media/shows

Change your folder name to Season 1 and see what happens.
Your probably also need to do S01E0# in the file names too.

Agreed, you could do something like this too (using BoB as an example).

/media/Shows/Band of Brothers/Band of Brothers - S01E01 - Currahee - [imdbid-tt1245384] - 1080p.mkv
/media/Shows/Band of Brothers/Band of Brothers - S01E02 - End of Days - [imdbid-tt1247465] - 1080p.mkv
etc....