(3) a few prints on boxes left behind by a guy who worked in the building and was moving boxes every day.
Here's what you're missing, though...
On one of the Rolling Readers boxes at the window, Oswald's left palmprint and his right index fingerprint were found.
The employees laying the floor moved the large boxes of books from the west end of the floor over to the east end. However, the "Rolling Readers" boxes did not need to be moved, i.e. they weren't over on the west end where the new floor was being placed down. The two "Rolling readers" boxes in the sniper's nest were originally about three aisles over from the sniper's nest window and were taken to that window for the purposes of being used as a gun rest. The "Rolling Readers" boxes didn't contain books.
Other identifiable prints were developed on the boxes. These prints were compared with the fingerprints of all other employees as well as law enforcement personnel who handled the boxes. None of the identifiable prints belonged to any of the other employees.
So, the Rolling Readers boxes were in the sniper's nest and used as a gun rest. Oswald's prints were on one of these two smaller boxes. No other employee of the building had their prints found on either of these two Rolling Readers boxes. These two particular boxes wouldn't have been moved there by the floor-laying crew (having been stored about three aisles from the sniper's nest, they weren't in the way, like the bigger boxes over on the west end were).