I just disconnected the PAIR plumbing on my Gen 2 last night and that's what the connector on mine looks like except on mine it's on the other side of the bike close to that air box nipple.
Can't tell what you are pointing at in the picture below that one - throttle position sensor????
No idea on the buried yellow plastic fitting in the last pic.
I love the labelling of the various bits. Very nice when working on the bike. I wish the previous owner of my "new" 2011 had done so on the auxiliary wiring. I may just rip it all out and start over!