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Hey thanks! Interesting that it is applying the lighting at all! Overriding shouldn't apply the default shader and thus not apply lighting. What you can do is just call the function:

my_model = __FauxtonWriteSpriteStack(sprite_index, x, y, z, color, alpha, angle);
my_tex = sprite_get_texture(ico_texref, 0);

and then in the draw event call:

matrix_set(matrix_world, matrix_build(x, y, z, xrot, yrot, zrot, xscale, yscale, zscale));
vertex_submit(my_model, pr_trianglelist, my_tex);
matrix_reset();

and that will make it so that you only get the actual vertex buffer of a sprite stack instead of all of the extra stuff that Fauxton comes with. Then you might want to make your own shader if but it shouldn't be necessary. 

as for 'joining' models together, the system isn't built for that currently, but I have made it work with 'nine slices' before using texcubes. You would essentially draw each frame of the fence to surfaces, apply the surfaces to the texcube, and then stretch the texcube / surfaces. This way GM will automatically use its 'nineslice' feature and there you go! You have multiple 'fences' within 1 vertex model (so that lighting will work as a whole instead of in pieces). 

Hope this helps! :)