So I took Dives and Black_Stormy's advice and revamped the last room a little bit. Here's the improvement:

Also, I downloaded some custom textures and applied them to some brushes but in-game, they were are all 100% bright/lit (only the custom textures). I don't know what the problem was but if someone knows how to fix them, let me know please.
Edit: One problem though, for those light shafts that are projected from the ceiling, I used GCFScape to extract the .vmt files that were removed by Valve and I put them in my HL2/materials folder. My question is, if I were to distribute this map to someone, would they need these .vmt files extracted in their folder as well or can I just pakrat them?