So I want to create some eye textures that are asymmetrical, i.e. one eye is different from the other. I've looked at the eye textures of various mods on the nexus and they clearly only use textures for one eye, presumably both eyes using the same texture. So what I want to know is if there's any way around this to make odd eyes. The only idea I can think of is some sort of modification to the eye meshes (which I think are different for left and right) so that they use distinct textures. The downside of it being that assuming all NPC and actor eyes use the same meshes, you'd need to patch it up with duplicated textures for them so that you don't get NPCs running around with one normal and one textureless eye. I'm also not exactly sure how well that would work with selecting the eye textures for player characters in-game, since I have no idea how the character creation works. I'm fairly sure I've seen it work in Oblivion, but I never did much poking around with its mechanisms so I don't know if eye textures for that have both eyes instead of just one. It's not the end of the world if it's not possible but any help would be appreciated.

You are ritght, you need to modify the UV maps for the right and left eye meshes. That was what was done for Oblivion and has problems, like the ones you've pointed out: the new eye textures won't be compatible with the vanilla eye meshes, and vice versa.
To make your new eye meshes and textures work for the player and not interfere with existing NPCs, just create a new playable race that uses your eyes.

Hope this helps

I just remapped all 4 sets of eyes for this purpose. there will be a mod that does a replacer of the few vanilla eye textures- it shouldn't affect vanilla a whole lot. and also has a bunch of extra eyes for the player to choose. including hetrochromia

and also might replace the dogs eyes as well :shrug: