FINALLY! I got all the aft fuselage bulkheads, skins, and J-channels in and aligned at the same time. I was able to re-insert the F-779 with only removing the F-712. Most of the time was spent wedging the clecos into the row of holes common to the side skins, bottom tail skin, and the bottom J-channel.
The next work session I'll invert the aft fuselage, square it up and start drilling. To keep everything lined up I'll remove one cleco, drill the hole, and then replace the cleco before moving on. This will be extremely tedious but should hold everything in position.