@boomerang,
Yep I'm worried about that (poop and pee). When he gets nervous, he poops that could be a bit gross. Must be why the airlines require a waterproof bottom to the carrier.
I was warned against the sedative actually by the airlines as this could impact a dog's breathing.
We also plan to bring him to the park and let him run around before flying. Something like we used to do with the kids when they were toddlers.