As a part of my notes, I also write the story itself. It helps me establish my voice, and gain hands-on perspective about how the character is presented, but, while this is helpful, I cannot craft a masterpiece on a linear path of construction.
Please note that, while my advice listed above is my own, there are many who work the same way. It doesn't matter to me if a story is published or not, but if it has stirred and inspired the masses - made people think. There are the examples I use for research. Not that I'm saying a timeless story couldn't be crafted in a rush from a singular idea (The Old Man and the Sea was crafted that way, I believe), but I will say that I believe many more great stories have come from writing from the inside out.
The construction of the story treatment is much like the same approach to writing a story, but decidedly shorter, maybe at 1/10 the the size of your narrative. You still let characters and situations guide the flow of the story, but you are working with a much more concise a space to change your story, which is completely written, even with non intra-scene pacing. Pacing IS guided by characters, but many make the mistake of becoming defensive about their pacing, claiming that it flows from the characters and their conflict, but they are simply failing to see the human rhythm that the reader comes from, that is, wanting a change of pace: action flow in time, sentence length, paragraph length, narrative-dialogue balance, etc. There are many effective stories that don't have good pacing, but they seem to win awards and then get relagated to the second-best shelf, so to speak. Either that, or they isolate some people who are sensitive to pacing, who toss the book across the room with force if they are given half a book of boring introduction, or 400 action-clogged pages. Pacing helps draw emotion into your story, and it helps create a connection of trust between you and your reader.
I'm sorry if my ideas about constructing your story before your pacing detail are offensive, but the truth is that this is part of the phenomenon of second, third, and forth drafts - rewrites, revisions, and extensive editing in any form. We all seem to go through this process of knowing our story and world, and out of that knowledge comes a truer version of the story our story is trying to be. Sometimes we make it, others no, but that should be our goal, and though there are different methods to get to that point, there are different methods to that same end of knowing our story.
My recommendation, however, is to start with practice story, notes, drawings, notes, notes, and more notes, move it to a 10-50 page treatment, then give it flesh, life, and, accordant with this thread's topic, pacing. Our only hope is that the readers pace along with us.