I had the same problem with a biplane that I built a few years ago. The bottom wing was off to one side so it really messed up all the alignment for both wings. I finally rebuilt the bottom wing and allowed for the mistake on the plans and all came out fine in the end. I have since learned that I need to measure the plans to make sure they are good because I have found this issue on more than one set of plans. It shouldn't be an issue for your Cub as stated above however as they fly really well.