Here is a video since I can't explain well through text. If anyone knows how to fix this it would really help.
https://www.youtube.com/watch?v=PzEzUBsjbCM

so your problem is that you dont have model lighting? (i could hear the video lol) first of all if you made a light grid brush it must just vover wheret he player will be moving, nothing else and it must have the lightgrid pink texture, also you need to add an skybox made of brushes to make the sun work in game

I have the infinite skybox added thought a script.

I have the infinite skybox added thought a script.

you need the brush one anyways i said!!!ok jk
but yeah you need to make one made by hollowing one big box and applying sky texture to the inside faces , to prevent bsp leaks and to make your sun lit the map, otherwise there wont be any sun

looks like its that time of the year again. time to re-install mod tools. backup the maps with toms tools

I just make a backup of the main map file and patch. Works the same for me.

looks like its that time of the year again. time to re-install mod tools. backup the maps with toms tools

I've been using the same Mod Tools install for 4 years now 

I dont think that "fog" clip does anything, you need to add fog through FX, also for light you need to have a light grid, not sure if you have that or not, I recommend copying your .map files to somewhere safe and uninstalling all the mod tools then reinstall them again

I dont think that "fog" clip does anything, you need to add fog through FX

in fact it doesnt lol i think it has or had some usage as the foliage clip which made you invisible to the enemy ai.