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The ones I know of, and have in my reading list are James Madison by Brookhiser and James Madison by Wills. I don't think I have come across the definitive ones but these at least take Madison out of the context of the Constitution and away from Jefferson. His close association with Jefferson has often overshadowed Madison, in my opinion, so it's often hard to hear much about him without Jefferson's shadow being in the way. I've come across some bits on Madison when reading the John Adams and Alexander Hamilton biographies, and I've been interested in reading more about him and his background and these two books cover much of his philosophy and thinking.
Edit: This new book Madison and the Making of America seems to cover some of what you were looking for as well.