Now that I think I am finished with the aft fuselage and bringing the wires forward, I went ahead and installed the transponder right behind the baggage cover. That way it will be easy access when it needs maintenance. Then I ran all those wires up to the panel. Here you can see the location of the transponder and the shelf in the back with the magnetometers on it and how neat the wires are.
I only have those two white wires on the left from the elevator trim that I have to deal with. I think I will bring them up the right side of this picture and insert them into the molex connector on the pilot side.