Flowers from the Storm, which is the one with the Quaker and the mathematician aristocrat who has a stroke and loses the ability to speak for a while.
The Shadow and the Star, which is the one with the boy prostitute who became a ninja and the dressmaker.
The Hidden Heart, which is the one with the heroine who grew up wandering the wilderness with her scientist father, then hooks up with a privateer, and there's also an Evil Other Man, and she rescues a boy prostitute, the one who later becomes a ninja.