Thanks for the help.
I dont feel that it is a structural issue though. With the seams stitched, if I lift up on the port stern corner, this side of the stern will stay raised up higher than the starboard side. Same if I lift up on the starboard stern corner, it will stay raised up higher than the port side. She does not want to force her way back into a certian position, and will stay where it was last set. The stern corners will also move slightly up and down if I twist the bow. I was wondering if there is a way to measure this, or some trick to the trade on squareing up the stern with the hull and bow, and if there are any other alignment issues that I am probably missing?
Thanks again