Yeah, the layout is changed a good amount in mine, I was unaware of the other mod out there. I'm new to Source modding in general, in the past I made huge expansions for Morrowind and other games, but since this is my first map with Hammer I was just trying to learn everything. You can download the map here:
http://homepages.nyu.edu/~pes226/cs_cbble.bsp
and the nav file here:
http://homepages.nyu.edu/~pes226/cs_cbble.nav
When you run the map it will tell you the nav file is from a previous map. It definately works, but I thought I was done when a few problems popped up, and I have to hand tweak the nav so the hosties dont get lost easily, so it takes a while and I haven't gotten around to it yet. I also figured I might make changes based on your suggestions so an updated nav would be wasted effort. Let me know if this works or if I uploaded the wrong things or if somethings missing. Thanks!