The first thing is the spring which holds the air filter in place inside the airbox.
I think that the 2 lines might be for vacuum to the petcock. I think one is always capped and the other is connected to the petcock if the petcock is the type which uses vacuum to open the flow of fuel. Since you have a secondary, down-line fuel shut-off, I suspect that either your petcock was replaced with a non-vacuum one, or, it no longer operates properly. In either case, the 2nd vacuum line would need to be capped too.