I didn't know that bags have to be picked up at HND. Is that a general rule in Japan, just like in the US, that at the first port of entry checked bags have to be picked up to go through customs and then can be dropped off again (if tagged through)? Or just an incompatibility with the international-to-domestic connection?

My main concern is that the bag may be larger (and definitely heavier) than the Japan Airlines policies for carry on luggage allow. I doubt this will be enforced for business class passengers departing the US, but might be an issue at HND. I suppose my worst case scenario would be if I was made to leave the secure area, find my way to the check in counter, etc., then re-clear security - I will have slightly more than 3 hours but would prefer to avoid this as the tickets are separate. Hopefully if I made it to the departure gate, the HND gate agent would just confiscate the overiszed bag at the gate and check it in at that point?