I always had problems with what to do with my head, i was taught to take a breath on the side, then exhale it with your face down in the water, then repeat, but kicks and arm strokes I never had rythm problem with
The difficulty (as I learned after my lesson today) is multiple. The 's' shape that your arm is to move in, the way the body turns in the water from side to side, etc.
when I swam, of course everything is natural. What you need to do is do exercises that concentrate on one thing. Do a set of breathing every 3,5,7,9 strokes. Then work on arm pull, etc...