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Add a piece of trim at the top of the bed box to match the trim on the tops of the bookcases.
Fill the recessed holes with wood putty. Also fill the nail holes on the trim pieces, door panels and the small seam along the sides of the bed box.
Lightly sand the footboard and use an orbital sander on the bed box. Wipe away residue, and add primer to both pieces.
Paint the footboard to match the bookcases (image 1). Then paint the bed box to match the walls (image 2).
Hold the bed up and install some simple sliding bolts inside both bookcases. Drill a hole through the bookcase into the bed box, and screw them into place. Place the bolts underneath the shelves so they are completely out of sight.