As Paul Harvey would say, here is the rest of the story.
Sunday was de-construction day. But first I did the only thing that made sense after after a major screw-up. Throw a party. Saturday night was a good night to build a fire and invite about 20 - 30 friends over to help drown my sorrows in adult beverages.

After a short recovery time Sunday morning it was time to get to work.
I started to very carefully remove the ceiling with a hammer and chisel and soon found that my rubber mallet alone was much more efficient. As I suspected this left the spars covered with remanents of plywood and glue. I also had glue on the walls where the bulkhead was attached. Now to clean up the mess. halfdome, Danny suggested making a base for the router and using it to remove the residue.
Brilliant! It worked perfectally. Stripped off the glue and left a good surface to accept more glue. I used the same idea to clean the spars. I clamped a dummy spar next to the installed spar and then used a flush trim bit to clean it up. This left only a small amount of hand work next to the walls.
With everything cleaned up it was time to get things square again. Gerdo suggested putting in the bulkhead first using it to square up the walls.
Brilliant! I rebuilt my bulkhead out of 2 X 2's making sure it was square. With it screwed in place I checked the length and diagonal measurements of each spar. Everything looked good but the very end of the rear walls were still slightly out of square with the floor. However the spars were square with the walls. How could this be?

After a lot of head scratching, we, that is my better half and I, determined that part of the problem was the floor and the other part was a slight warp to the walls. I temporarily installed my counter top and realized that when I screw ithe walls into it they will be pulled into line. I then glued and screwed the new bulkhead into place, installed a cabinet top/shelf, and a second shorter bulkhead offset to the rear. I'll get pictures of this posted to my gallery in a day or two so you can see what I'm talking about.
That was enough for one day. I had learned many new words along with the new skills kayakrguy referred to, referred to, and was getting tired. Not to mention that is was getting close to time for my Colt's to take out NE. Couldn't miss that game. Later today I hope to reinstall the ceiling and I will be able to move on.
I have got to say a big thank you to all of you for your help and encouragement. I had at one point considered gas and a match as a solution. No not really. But things are looking better and my spirits and confidence are back in place. The Earth will continue to turn, and my TD project will move along. Thanks again guys.