Don't let another nation take leadership of the war. If you are a European power, by the time you reach Japan you should have technology superior enough to destroy all of the islands' defenses without the help of allies. If you really do need alliance help to overtake the islands, try to bring in only nations weaker than yourself; a stronger nation will usually take leadership of the war.
I believe that in DW the Shogunate system may do something odd regarding infamy, so you might want to dismantle the Shogunate before actually annexing territory. Not entirely sure how that works, as I have yet to invade Japan or play as a Daimyo.
I phrased this poorly, I meant an ally of Japan assumes leadership, and I can't access negotiation options for anyone except the leader. If I negotiate with the single province Japan, I can't actually take any provinces, and I can't negotiate with the larger states.