First let me say great information on traveling with pets. 2 1/2 yrs ago we moved to Japan from GA with 4 cats and a dog. We are going to be going back to the states in a couple of months so I will be able to tell you how that goes soon. Please note that there are quarantine rules to bring pets into Japan. If you are coming to Japan start 7 months in advance to avoid having to quarantine your pet in Japan. Here is the website:
http://www.maff-aqs.go.jp/english/ry...rt/dog-cat.htm.
We flew United from Portland to San Francisco to Osaka to Naha (Okinawa). There were only 4 spots to take them as checked baggage so I also carried one in cabin. There is a limit in the number that can be fly as checked baggage. I did have to take her out of the carrier at security in Portland, they let me take her to a room so I did not have to take her out amongst all the people but this is not always possible. Chicago made a friend take her 3 cats out right there amongst all the people. One idea I have is to take a laundry bag that you use to wash lingerie, put your cat in that and walk through the metal detector with your cat that way. They could still see the cat and it could not get away. I have not tried this but will when we go back to the states. In SFO they let me see the pets I had in checked baggage and I was even able to take the dog outside to go potty. They did have to check the animals through security again after I touched them. Osaka is where I went through customs and cleared quarantine. This took about 15 minutes with all five animals. I had emailed them before I left and they had all the paperwork ready to go. This is one of the nice things about Japan; they are organized and very courteous. Make sure you have the correct microchip in your pet. They can only read international microchips. I carried a scanner I had rented from Avid. Another note about flying from Japan to the island of Okinawa do not book a flight that takes you from Narita (Tokyo) to Haneda. This involves a 3 hour bus trip. There is one flight from Narita to Okinawa or go through Osaka.
United is partnered with All Nippon Airlines (ANA) in Japan. They do not allow pets in the cabin. I carried a hard sided carrier with me and put the cat I had in the cabin into that carrier. You will get your luggage in Osaka/Narita so be prepared to handle pets and luggage there. You will have to pay again in Osaka/Narita to get the pets to Okinawa. This is based on weight. 24 hours later all five pets arrived safely in Okinawa. This was a very stressful experience but with a lot of planning things did go quite smoothly. My advice is plan every little detail.