Okay, I checked the TexGen output folder, and inside it was a rar/zip archive of the same name, so I unzipped those contents into the Texgen Output folder like so:
before:
TexGen_Output (folder)
> TexGen_Output (zipped archive)
> textures
after:
TexGen_Output (folder)
> textures
After doing that, it seemed to have found them and gave me the large references error (which I can fix myself) I will update soon. I don't know why it was zipped inside of the folder, but I dont think I will zip them anymore.
UPDATE 7PM CST: I got it all working now. I was zipping the Texgen folder when it was already zipped inside, instead of adding the already zipped archive inside of the folder. I had been doing it like this for years since I was using Mod Organizer 2, and had no issues before until I started using Vortex.