Are you using the latest UrT? I'd guess so but I've heard about missing textures if you aren't. I did a really poor job of art asset management
I just picked willy-nilly from everything that got loaded into radiant and man what a pain that was to pack. On the map I'm working on right now I cleaned up shaderlist.txt before I started and I've kept track of where everything is coming from.
Man.. thanks for noticing the glass roof. I love that thing. It's a lot of fun from a gameplay point of view too. I learned a lot about clipping brushes and keeping things lined up on the grid, etc etc. doing that.
I used to run it on my server when I had one. Boooo it sucks not having my own anymore, otherwise I'd offer it up for you to test your map on and we could try 'em out