Based on the gen5 that I have:
Left tank hose: Breather Hose (somewhat important)
Right tank hose: Overflow Hose (runs to charcoal canister, a non-functional piece of government mandated garbage)
Don't cap it off, just don't fret about nothing being attached to it.
The middle airbox screw/bolt is important considering it's the only bolt that holds down the air filter. I personally would replace it via Partzilla or simply run to the hardware store. I doubt those screws are manufacturer specific.
When in doubt... send it!