Hi Monica - deleting the top planar face and then reconstructing it by selecting the existing edge curves and running Construct > Planar seems to solve the joining problem.

But it would be easier to finish up the model if it was in the pre-boolean state before the hole was opened up in the side. Do you have a version of this file saved off before it was cut by the circle? If so please post that one so I can repair that version and then the boolean with the circle cut should work properly after that.

- Michael