Personally, if I can see a misalignment during build/assembly, I fix it. Doesn't matter if it's a Cub or an aerobatic plane. When I pull back on the stick I want a loop, not a corkscrew like Richard described. Choose the method which seems best, and deal with it. From everything you've said, it sounds like you've identified the wing tube as the primary cause. Maybe some pics of that area would help people suggest a fix that's not as bad as you think it will be. Note, you can post pics in a thread too. Use the add reply button, instead of the quick reply box that's at the bottom of the thread. Then hit the "Click here to upload!" link in the bottom left corner of the text box.