We made it! The last step of the process! This one is time-consuming but by far the most fun of them all.
All those post-it flags and notes in the margin? They're coming off.
First, the easy ones. Whatever colors you've designated for things to move elsewhere (4 out of 6 categories) are the ones you'll go through first. Go one color at a time and start cutting and pasting. This is where your margin notes will come in handy. You should have noted along the way where to move something to. Mine read something like, "Use this scene for such and such bit of mythology, character history, whatever."
As you address each of these changes, remove the post-it. This pass-through will leave you with just two colors and two categories to address: Scenes/chapters to reconsider (which I've marked in mine with orange) and things hinted at or foreshadowed that need to be developed further.
These two are the meatiest of your categories and the ones the hardest and most time-consuming to address. But your outline will work for you, not the other way around, with this method. This outline will help you to close up plot holes, deepen characters, adequately foreshadow events, etc.
The easier of these two categories is the foreshadowing/developing further one. For each of your post-its in this category, go back through your margin notes. These notes will indicate places where it will flow naturally to put in a sentence, a short scene, anything that might help foreshadow without giving away or places where a small bit of backstory can be seeded to explain something you've indicated.
Don't remove the post-it until you've fully addressed it. This includes scenes that need to occur after the post-it, further on in the narrative. Once you feel that you've added everything that needs to be in order to smooth out the plot bump, you can remove that post-it.
Now we're only left with one color. Scenes and chapters to reconsider. You may find that many of these are no longer something that needs to be addressed and the post-it can be removed. (Many of mine ended up being deleted as I went through the other five categories of changes.) But this category also includes the scenes that you noted in the margins to add but don't get addressed by the other five pass-throughs.
In the end, you'll end up with a stronger story and a post-it free outline. (At this point, for future revisions, I would suggest you create a clean outline to work off. This one you've just finished with is vastly different from the manuscript as it currently stands.)