Some good ideas and advice here from people who have done this or something similar but the obvious people to answer many of these detail questions are the people managing the livestock plane.
Flight time may be 5.5 hours but what time is drop-off and how soon can you pick them up. To me that...
I'd talk to the airline and see what they suggest for crates. They are going to have rules that you have to follow. Find out what they are from the airline. Another good source might be your extension service. You might call them and see if they have anything to offer.
What is the flight...