".....It should be the wiper motor but I do not know what is all missing from in there. Next to the wiper motor towards the drivers door is another square open area with what looks to be some kind of box with nothing in it....."

Yup that's the wiper motor. You don;t appear to be missing anything, the wiper motor is self contained. As far as the other opening, they are there to provide access to the windshield hinges.