Just completed the exact same conversion. It left me with one hydraulic line going to the rear brake through the frame, one hydraulic line to the front brake via a fork leg and one Di2 wire going from the A junction box into the frame via one of the ports in the head tube.
BTW, this is an Ultegra installation. I've run a Campy Record EPS v3 group on my other bike for years, and for my money, the Di2 set up shifts more cleanly and quietly by a significant margin. Forgive me this piece of blasphemy, but it's true