Sadly, I haven't yet. Sorry I took so long to respond. I didn't know I had a new reply. I'm sorry you're having trouble with the mod, too. I didn't know there were others that had the same problem. That's the part that puzzles me. I don't know why other people's computers can load the mod perfectly, while some of us are having trouble loading it right. I'm wondering if there's a file in SSE that needs to be configured, so that mods could be read in the folder its supposed to be. It just seems so odd that other people haven't had the same problems we've encountered, especially when we followed the steps right.
Now I'm wondering: which file in SSE is responsible for reading the mod folder?

Which missions folder did you use? The one inside the game install directory or the one that you can find under "...\AppData\Roaming\Nightdive Studios\System Shock EE\missions"?

My System Shock EE folder is not even structured that way. It's not "...\AppData\Roaming\Nightdive Studios\System Shock EE\missions"? It's more like "GOG Games\System Shock EE\res\missions." Everybody else's computers seem to structure it with the AppData part. It's always installed differently me. I tried installed SSE through GOG Galaxy, and it's structured the same, and it still doesn't load the mods. However, I haven't tried GOG Galaxy 2. I've tried loading the mod with the Steam version, and it still doesn't show. I don't know why your computer installs the game that way, but it doesn't do so for me. How are the files arranged on your version?

That is exactly what Berzerk is saying. The question was if you used the missions folder in the game install directory (for you "GOG Games\System Shock EE\res\missions") OR the one in "...\AppData\Roaming\Nightdive Studios\System Shock EE\missions" (which is not the game install folder).

You can access that path up to the Roaming folder by simply entering %AppData% in a Windows Explorer address bar or a "Run..." prompt (at least in Win7 and above).

Well, no wonder I was so confused. That was a step that was left out. I didn't know that the Appdata could only be accessed that way. Now the question is, why did the modders and developers design it so that you can only load mods that way? Why not just load it at the main missions folder? It seems counterintuitive to me, but at least I finally got to see how it worked. Thank you, Links! Now, I'm able to load Ruby Station, but I'm still having trouble with Rewired. I'll just fiddle with it some more. [Edit: Nevermind. I finally got it working] It's just a relief to be able to get it working right. Again, thanks.