After reading a few other builder logs to figure out the best way to fit and drill the aft fuselage parts, I decided to fit the lower skin since it is a set dimension. It fit nicely and was easy to pilot drill. I turned the aft fuselage upside down, taped the skin tight to the fuselage sides and drilled.
I do have a little sagging of the skin between the lower cross ties. This is the only thing I'm disappointed with. With the dimension being set, I don't see how the sag could be taken out, so I'll have to play with that a bit.