So this topic has had very little attention, but it's given me time to break down my "problem". I believe I've come to a conclusion about what exactly is wrong, so I'll offer my explanation below. If you don't know what's going on, scroll to the bottom of this post for a quote containing my original message.


Conclusion:

After (literally) 24 hours of non-stop experimenting, about 10 oblivion re-installations and TONS of esp/Bash edits, I've discovered that my mod was in fact working the entire time.

It seems that TES CS seperates custom eyes from preset Vanilla NPC eyes until it's told to do otherwise. For example, let's say I remove the default Vanilla eyes from TES CS's Body Data window. Now, let's say I replace all of those eyes with my own texture, "BlueEye.dds". When I look in the FaceGen Data tab, I will see my textures appear fine. Also, when I log into Oblivion and create/edit my character, I will have the option to use my BlueEye.dss texture on the eyes. However when I approach an NPC, I'll discover that their eyes have not changed, or that very few have.

Now let's say that I go back into TES CS and check to see if my textures are still the only eye textures loaded in the Body Data of all races. I want to see Uriel Septum (The King, and one of the first people you meet, if you didn't know) wearing my eye texture. I would go to the "Object Window" box, click "+Actors", "+NPC", and then scroll down until I find his name. I would double click "Uriel Septum", upon which his information and edit box would pop up. If you go to the "Face" tab here, you'll see the eye texture has now taken effect, and clicking "Ok" and then saving your plugin will apply these changes. Uriel Septum will now have my eyes in Oblivion.

My theory on how this works is that NPCs have preset eyes, since NPCs themselves aren't randomly generated. This accounts for most of the NPCs not having my textures, and several "random" NPCs with them. When you double click to edit the NPC in TES CS, I believe it applies your own personal loaded textures to the NPC being edited.

Oddly enough, if you're in the Race menu and you edit any of the meshes in the "Face Data" tab, it will be applied to every NPC in the game of your selected race.

Since I'm not an experienced modder, I can't verify any of the above information. I can tell you that it appears as if textures are not shared to NPCs, but meshes are. More than that you'll have to discover on your own, or someone will need to reply to this topic with professional information. I can only hope this has helped some other weary soul who's gone through this level of hell. Enjoy!