Book structure can be such a fun dilemma. Placing events and scenes strikes me as similar to the grid logic puzzles in which Sally might live in a red house but only if Johnny wears a bowler hat and Susie drives a green moped to school.
(Imagine my joy when I found out that the LSAT, which I sat for in 1990, included a section of logic puzzles to solve! Alas, I realized that, while I would have made an excellent lawyer, the idea of law school itself felt like a chore, so I declined admission. One of the many untrod paths diverging in my yellow woods.)
While life (and life-in-narrative) proceeds in linear fashion, books themselves do not need to tell the story in a similarly straightforward way. (Consider the lyrics from the old Blues Traveler song: "I hope the past is behind us. Be real confusing if not.")
Grab a pad of sticky notes. Choose a single color of note, and on each one, write down the name of each key scene/event. (Key scenes = what must appear in chronological order, though of course other scenes can and will happen between them.)
Once you have them all down, arrange them in chronological order in a line on your wall or floor—wherever you have room to see them in one continuous timeline.
This timeline provides your foundational structure. No matter what happens between these scenes, readers will easily follow the narrative's logic.
Gather the pages that correspond to these scenes. Create a document of just these pages, and read it from start to finish. Does it make sense? Is it clear? Has anything been forgotten? Does anything repeat? Does Chekhov's gun need to be placed in an earlier drawer? Do you have other sections that also need to be included?
And so forth.
Once you are satisfied with this structure's coherence and completeness, you are free to add in the other scenes.
Use a different set of colored sticky notes to place on your timeline. (You can divide these colors by character as well if that makes sense.) These notes can (and will) move around as you continue adding to the draft manuscript. As you add logical groupings of sticky notes, add those corresponding pages to the draft and read again start to finish, making notes on the same questions of logic/holes/repetitions.
This is, of course, just one idea for keeping your structure's integrity. Chapter titles can also do wonders to orient readers without the need to include mundane transitional material. Eventually, you'll have a fairly complete draft and a clear idea of what can be deleted, compressed, and added.
