Several incoming Kumamoto JETs have been inquiring about the process of flying to Kumamoto after Tokyo Orientation. Flights for all incoming JETs have been booked and together with the Kumamoto PAs, we will be traveling as group together from Tokyo Orientation to Haneda Airport and onto to the plane heading to Kumamoto. Once we all arrive at Kumamoto Airport, you will then meet people from your specific placement and head with them there.
As for baggage, the rules for flying domestically in Japan apply. You can find the rules for ANA here: http://www.ana.co.jp/wws/japan/e/local/domestic/prepare/baggage/?menu=baggage-rule. However, please be aware that in previous years, incoming JETs have been asked to come to Tokyo Orientation with only one carry-on and one large piece of baggage. Any other pieces of baggage you bring with you from abroad will be collected at Narita Airport when you arrive and will be sent directly to your placement in Kumamoto.
Update: A previous version of this post linked to the baggage rules for Japan Airlines. Incoming JETs will fly on ANA and the link has been updated.