1. You just need a path_track for the train to pass at some point to tell the gates (output OnPass) when to open, and preferably for the signals to sound and light up too!
2. Skyboxes trains are seperate from the normal ones.. and valve made some crazy logic cases and things for that transition. If you are making them continue in the skybox, then I would say yes copy valve's and tweak to your need, as it will be a lot more effort to make from scratch. Just try and make sure you understand what it all does!
3. As you probably saw from Well, the skybox are just tiny props that go on their own path_tracks.