I've done five trips to the Pinehurst area. You can have a complete and satisfying trip playing Mid Pines, Pine Needles, and Southern Pines.
I'd suggest that for the 36 hole days you try to play Mid Pines and Pine Needles with 18 holes on each course. All you have go do is cross the street to get to the other course. I played Southern Pines during the renovation, just after it reopened, and again in March of this year. I'd play it on the days you plan to play 18 holes so it's likely that pin positions will vary. On the March trip this year I also played Mid Pines and Pine Needles. Despite the common heritage of each course, it's not like you get the feeling you are playing the same holes so there is less of a deja vu sense of what you might encounter with the work of some designers.
I also like the distinct character of each course and club. Despite the presence of the Pinehurst Resort in the immediate area, you can have a high quality golf experience at the three courses you are playing. I've played four of the resort courses and liked the experience.
Charles Lund