Is it possible that as you were sewing the feed dogs fed the fabric on the bottom a little faster than the fabric on the top, so you actually have more fabric on one side than the other? This probably is seen frequently when sewing longer pieces of fabric, and I think that's the usual reason people have for sewing every other row in the opposite direction. Now that you have ripped out every other seam, can you press the pieces so that they lay completely flat? If so, I think you will be okay, but you might try using the walking foot to do the remaining sewing. Also, pin the pieces together in several places so that one side doesn't feed more quickly than the other.