The Confusion is, almost entirely, about Jack and Eliza and what happens to them over the next umpteen years.
Daniel, while he has a few appearances in Book 2 (in the Eliza sections), doesn't really appear until Book 3, when he winds up, effectively, being the prime mover of a whole host of plots.
Unfortunately, I'm not real sure if there is a Plot to tie everything together, other than that you're witnessing events over a great span of time and distance that're pretty cool. But, I have to say, I really did enjoy the series.
Brad