Ok, I'm making a map that is using custom textures so I have a textures/mytex folder in my pk3 with my custom textures. I also have a custom shader I'm using for the sky, but instead of custom sky textures I want to use the yavin sky textures. Here's the problem: my sky shows up as the texture missing grid because I believe it is looking for the yavin sky textures in my texture directory in my pk3 instead of the assets pk3s that came with the game. I do not wish to include the yavin sky textures in my pk3 because that is redundant and increases filesize. Is there anyway to work around this?

It always looks in the assets#.pk3 files...always.

Have you made a custom shader that references the yavin skybox files or are you using the shader that came with the game?

this is what my custom shader looks like:

textures/tristan/yavin_sun
{
qer_editorimage textures/skies/sky
surfaceparm sky
surfaceparm noimpact
surfaceparm nomarks
q3map_sunExt 0.903380 0.983185 1 100 135 25 0 12
q3map_lightmapfilterradius 0 128
q3map_skylight 200 3
notc
q3map_nolightmap
skyParms textures/skies/yavin 512 -
}

Ok now is that in a new .shader file and if it is, have you added the name of that file to shaderlist.txt ? Shaders will NOT be parsed if they aren't in a file referenced in shaderlist.txt by the compiler. The game doesn't need shaderlist.txt but the compiler does and any shaders that have compile-time arguments (sky shaders do) must be in it.

Yep, it's named tristan.shader and I've added it to the shaderlist.txt.