Glad to hear it! I definitely know the feeling of coming home with a new rental and being frustrated that it's not behaving the way I want out of the box. Nikon bodies give you lots of knobs, buttons, and wheels to fiddle with, so don't worry if you're not totally comfortable with it just yet. A good amount of the controls do rely on being able to use your left hand, but it's not too bad once you get used to it.
Another point to note about the ISO selection is that I use Auto ISO in either Av or M mode almost exclusively. You can set a minimum shutter speed based on the focal length of the lens and a maximum ISO value. Exposure compensation also works in any mode with auto iso enabled - you can even set it to be changed with the secondary dial in Av or Tv mode (whichever dial is not currently being used) without needing to press the +/- button. I usually don't worry at all about ISO as long as it's at 1600 or below, and I can see the current value of the auto ISO through the viewfinder, so I know where it is at all times and whether or not I need to adjust aperture/shutter speed.
That's just my perspective on the ISO controls, since I like to be able to control my DOF and shutter speed without bothering with setting an ISO for every shot. If i'm outside shooting landscapes and have time to set up in between shots then I can easily turn off auto ISO with the front Fn button that I mentioned earlier.
Edit: I think the AF controls should be quite straightforward. I stay in continuous mode all the time, as I haven't noticed any significant differences in accuracy between single-shot and continuous, even in very shallow DoF situations. This allows me to switch between single point only and full 3D tracking with the press of a button. I don't think there's any reason to use any of the intermediate settings, as 3D is the only setting that allows the camera to use information from the RGB metering to aid in AF tracking. In the case of the D600 i believe you would set this up by going to AF-C by holding the AF button and dialing it in with the rear wheel and then choosing between single and multi-point with the AF button and front wheel. You shouldn't ever need to change the point expansion setting away from 3D tracking.