Okay, so the eyes work in HLMV. But they get distorted in garry's mod when the model is used as a player model as well as sometimes when the eye poser is used on the ragdoll. I'm also having problems with a mesh deformation around the pelvis, as some verts just stop being bound to any part of it. The especially strange part is that the strange deformation stops when I use the model as a player model. I request that anyone wishing to help would message me instead of replying to this thread, then once it's finished we can post the solution for other people so the thread doesn't get messy.

Eyes, eyes, eyes. The most painful part of exporting to source.
It's either they're upside-down, multiplied, or the iris disappears.
I need to talk to someone about this. Please contact me if you have done eyes before.