Finally got around to checking the latest version out. The barn looks really cool. There are a couple reasons why you're struggling to get this to perform and light correctly.
1) There are holes in the map (leaks). It will not vis or light correctly with those present, so ALL geometry (even stuff outside of the map) will always be visible. You can fall through the ground in the tunnels and such. Make sure your map is sealed and keep an eye out for the "leaked" message when compiling.
2) Lots of gaps and such prevent any area from being invisible to other areas. For example, there is a gap between the roof and the wall, so pretty much everything on the inside is going to be visible from the outside and vice versa. Cracks in the wall and such will also cause problems. Try to make everything as sealed as possible and consider what is going to be visible from each location. Many maps employ giant "vis blockers" -- walls that completely block line of sight from one area to another. Quake-based engines are much better suited to corridors and rooms. Try to design your maps like this, but give the illusion of outdoor areas, if that makes sense.
Not sure if you'll ever pick this up again, but another good idea is to name your map files so they don't get confused with the final version. Like "mymap_beta1.bsp".
