Now that the shelves are in, they didn't quite make it to the ceiling which is OK! We wanted to add molding from the beginning so they would look more built in rather than store bought. The total space from the top to the ceiling was about 1 3/4".
The sides of the bookcases protrude out just slightly farther that the middle section, so Joe cut some scrap board to fill in the space which allowed him to brad nail evenly without any gaps. He attached the scrap board with wood glue.
Next, Joe cut the molding (sorry no pictures) using his miter saw and the Kreg molding guide (life saver!!) and then attached it with a brad nailer.
We ran into an issue with leveling because either the bookcase is crooked or the ceiling slants. We decided to attach the molding along the bookcase and simply filled in the space between with more scrap wood and caulking.
Now all that's left is a fresh coat of paint. Stay tuned!!