So, recently, I have moved from Windows to Linux, I'm running Ubuntu 22.04, and all in all it has been a very solid experience. However, I decided to restart map making after I found Trenchbroom on the software store. The source port I'm using is VKQuake, which runs without issue, but whenever I boot up Trenchbroom and try to use VKQuake as the port for testing, it won't read gfx. Now, I did some digging around other places, and even on this forum and everything I read said to replace pak0, which I did multiple times, however it's still not running.

You should set proper game path in Trenchbroom settings and your Quake paks should be named in lowercase: NOT PAK0.PAK & PAK1.PAK, but pak0.pak & pak1.pak, Linux filesystem is case-sensitive.
id1 catalog also should be in lowercase.

Thank you!! You mentioning the game path made me realize I had set it incorrectly, and also that the Id1 folder was in caps. Everything is working now, thank you again!