One thing I can't really suss out just yet is if there is enough stuff in both Nagasaki and Fukuoka to justify a base-move between them. I do my best to move my home base around as little as possible.
Cutting down my time in Tokyo is always an option if I need to squeeze another day or two on Kyushu, but I definitely want to keep a chunk of time available there.
Giving some thought to the flight combo. Cost is definitely a factor for me (see OP). I'll figure it out

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Thanks for the comments, everyone!