Tell us more about your tandem and yourselves. Size? Weight? etc.? Our 1980's steel tandem was a real "noodle" with "tandem snake" (moving side to side rather than tracking a straight line) was a real issue. My shoulders always hurt more than on my single. Shifting cranks to Out of Phase help a lot. Our next bike was a very stiff Cannondale. Bars and stem were too low which caused some pain. Current bike is post 2009 Cannondale which is much more comfortable than either of the previous bikes.
Captain will be happier if bars are raised a bit and if the bars are the right width--should be same as shoulders. Some builders shorten the captain top tube a bit for a more upright position as well.
All the comments about tires and stoker movement noted above also have a strong effect on handling.