Each red AF point is an area that the camera thought was in focus. Keep in mind that if you focus and then recompose, the red point(s) shown in the image playback will no longer be over what they were over when the focus was locked - they'll be over whatever they were over after you recompoosed without refocusing.
According to Mastering the Nikon D7000 by Darrell Young,
If you are using Single-point AF or Dynamic-area AF, you'll see a single red AF indicator where the camera was focused when you took the picture. If you are using Auto-area AF you'll see all the AF points that were providing autofocus in your image.
You can't be in live-view to use the interval timer.
Take out of live-view set up interval timer options.
If you need live-view to frame your shots (maybe using a tripod and have eye-piece cover on), do that then switch from live-view and turn interval timer on.