Your texture baker is grabbing neighboring surfaces by accident. You need to adjust the ray distance or use a cage mesh. But more importantly, you should not uv like this, it's extremely inefficient. Look into trim sheets to understand the workflow. http://wiki.polycount.com/wiki/MultiTexture#Trim_Sheets…
You link seems to be broken. The first tutorial here should answer many of your questions http://wiki.polycount.com/wiki/Modular_environments For really large models, the key is to use trim sheets rather than making the texture maps gigantic. You can also add detail textures, but the downside to that is it's handled…