In many cases a possible list of available stations is told you near the end of your A school, you will be told then to possibly make a list from those available..and I have also been told by my son that some of those he knows were just assigned and no choice.
As for changing commands, I am not sure how that works or how long you need to be at one command before being able to transfer..I would guess you would have to at least get all your quals done..have no clue on how long that takes as an HM.
Also know that in many cases if married and under E5, family cannot go with you to Japan. There are exceptions, but rare.
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