With a post-1644 POD, have the Qing dynasty of China control the entirety of Japan for at least thirty years.
Depends on what you mean. If it's like Xinjiang (indirect rule enforced by permanent garrisons) then yes. It it's like Korea or Vietnam, no.Might be very hard. Does vassalage count?
The possibility of Qing invasion was present in Japanese minds in the 17th century, which is part of the reason why the Tokugawa seriously considered aiding the Southern Ming, and even without Japanese aid the Qing have various justifications at hand.Vassalage with permanent troops garrisoned? Might as well name yourself emperor of japan for the amount of hatred it will cause with the Japanese of the 1600s.