I'm seeing the same misalignment, and several others, on the same model. I'm a little ahead of you (painting the transom window frames before installing them), and I've seen significant misalignments on the bulkhead slots, transom side supports, and stern carving (that one is mentioned in the instructions, but still annoying). I've been posting progress photos and notes on tumblr. You might pick up a few tips, or learn from my mistakes, here. At the moment, I'm trying to figure out some of the details of painting on the transom, and I've found google image searches for "rattlesnake stern" to be very helpful.