Measured and squared the aft fuselage assembly today. Everything is coming out square and level. If most of the parts are built per the plans at the beginning, they assemble nicely and the overall measurments are not hard to obtain.
After drilliing the lower skin, I fitted and drilled the lower cross ties. I then drilled the aft mixer structure that you can see in the third picture. This really stiffened things up in the back.
Finally, I drilled the upper cross ties once I confimred, for the third time, that everything was square.
Now it's time to start working on fitting the Y tail sturcture, aft shear web and various other parts in the very aft section. I have the 2.5" measurement on the aft edges of the fuselage, so I just need to make sure all the additional parts don't alter that dimension.