Excellent stuff, but there is a problem with the lit alpha scissor shader; fog color is applied over the alpha areas.
The lit transparent version doesn't have this problem, so presumably, it is a case of oversight with a simple fix?
[EDIT] I have fixed it by taking the code from the working transparent shader and adding
uniform float alpha_scissor : hint_range(0, 1) = 0.1;
to the declarations, and
ALPHA_SCISSOR = alpha_scissor;
to the final fragment.
I also pasted the billboard stuff in there too, although I'm fairly clueless about shaders and just bumbled through this.