Not having a Nikon I can't be of much use about associated programs for the laptop, but Leon's idea is a good one especially for freedom from the laptop. Otherwise go with your idea of using a watch, but you need to keep on the ball or you will end up with images running over your alloted time. If you do want to try using a laptop you can probably use
DSLR Shutter from Stark Labs. I dont know what you could use for focusing except possibly DSLR Focus, but you may need to manually set some of the initial settings.