Induced drag is only produced when real lift is created. In 2D flow, when only the airfoil drag is given, there is no induced drag even for discrete lift coefficients. 2D flow assumes an infinite aspect ratio [which results in zero induced drag][1].

Your zero lift drag coefficient should be the airfoil drag coefficient at the actual lift coefficient at the wing station when the airplane is in flight. Do this for several stations over span since the lift coefficient varies over span. Plus the contributions of fuselage, tail and whatever is added to the configuration, of course.


  [1]: https://aviation.stackexchange.com/questions/58414/how-does-wing-aspect-ratio-influence-lift-and-drag/58421?r=SearchResults&s=1%7C57.6275#58421