So I have successfully made a ray the represents the mouse unprojected into the world, and now I need to check if that ray can intersect with a quad object, here is the code
Since you are using cubes, you can use the Ray.Intersects(Plane) method. You just need a few more planes.
Once you determine the first intersection point, then you can construct more planes for each perpendicular face of your cube. Then you can use the Plane.Distance(Vector3) (I'm pretty sure this or something like it exists) to make sure your point is between each pair of perpendicular planes. If it is not between them, then you can ignore the intersection.