Hah, yeah I understand how much of a mess this can be... I can upload a few shaders for reference if you want, but don't expect them to be standard vert/frag shaders, as they aren't actually GLSL. They are ShaderLab, which Unity then compiles to GLSL/HLSL (I will provide the generated GLSL scripts too). And since Unity supports tons of platforms and rendering options, the generated GLSL shaders can be rather... big.
I don't know how Plasma does its rendering, but I suppose it's heavily relying on multiple passes (one per layer) using very generic pre-written shaders ? Personally I simply write one single-pass shader per material (similar materials can share the same shader though, but all the notion of layer is gone), so it's rather different.
Also, I didn't write any code to handle lighting - I just specify my shader uses lambertian lighting, and Unity's shader library does all the tedious light computations (really useful to me since they generate correct code for forward/deferred/pixel/vertex lighting). This library is free to download too, so it's a pretty useful reference.
So yeah, I'll provide soon a few SL scripts, the generated GLSL shaders and a link to Unity's shader library. I hope it won't be too cumbersome for what you intend to do.