I'd align the vertexes on both sides before getting the body to join with the head. You can do it by selecting all the vertexes along the neck line and scale them down along the Y axis. Hope this helps.
That's not a problem, you can still cut the object, or delete a raw of faces along the neck and then align the vertexes and attach the two object together again. I always snap the vertex to the other point, just to make sure that all the points are aligned.