[Crizz]

For FPS:

I had the same prob with my very first DesertBase (released back in May or so). I´ve rebuilt the whole map and tried out a lot of "tricks" to raise FPS without having dense fog.
The result for the _final or _sandstorm version was in some parts better than expected. I found also a way to reduce final comp. time with nearly all brushes set to structural, therefore resulting in a more accurate compiling. And comp. time dropped from 4 days (for my very first DB map) down to 2.5 hours!!!
Things that help there (from my experiene but as your map is as big as DesertBase_final and has a tunnelsys some should help):
+ Build structures within the blocksize of 1024 (turn on the blocksize while mapping!: View->Show->Show Blocks)
+ Try to include Areaportals (therefore non self closing doors are bad, I got rid of this feature for my _final version as open doors don´t close portals!)
+ especially for your tunnel system -> build caulked (structural) walls along the edges of the blocksize and directly under the terrain, as the terrain patch meshes don´t block vis. This blocks off your vis and raises vis compiling a lot! It also raises the visdata size but don´t panic it helps ;-)
+ for some areas that never see each other try to place manual vis blocks, but this raises vis-compiling though pays sometimes.
+ use the regular caulk (I think you´ve done it) on ALL non visible surfaces. Even the smallest non visible side of a brush should be caulked.
+ leave all walls, roofs and floors structural (ok, except small walls and damaged roofs)
+ Hint brushes: Oooops never used them, sorry! So I don´t wanna talk more BS, loool!

hope this helps! some things will help you more than others but hey, I don´t know the .map file :-))))

Crizz