I have finished my map model, and got an error which said:

append face_shader_index ((findItem geom_materials geometry_objects[g].material[face_matID[f]]) - 1)

It turns out even though my +sky material ID is correct in my Material Editor, the sky itself is not under material ID of one, when I try to change it it says in the "ID" drop down box "No Name - (1)"... Also none of my other Materials show up in the drop down box... But if I select somthing else, like the ground, all of my materials will show up in the drop down box (other than the sky material)

WTF?!

could it be that you added a MSOM (multi/sub) into a single material in the parent MSOM? click parent all the way to the top and make sure none of your materials in that list say multi/sub object.

"click parent all the way to the top" All the way to the top of what?

when you first set up your materials you click standard and select Multi/Sub and then you add materials to that MSOM list. inside that list you might have another MSOM.

click "go to parent" until the button turns grey, i.e., you can't click it anymore.

in the upper right of the material slot area should be a button that says Multi/Sub. make sure that below that none of your materials in the list also say Multi/Sub. they should only have the name of the textures you made except for the very first one which should be called +sky.

if that's not the case and you get desperate, delete all your materials and reset the material ID numbers, since they are most likely assigned wrong anyway due to the error in the material editor

Thats not the problem :(... I'm going to try to delete the sky and create a new one... Anyone know of how I can do this fairly easily?

select everything else, it ctrl+I to invert selection...delete and create.