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Running an internal battery?
With an internal battery the A junction (normally placed under the handlebars) has the charging port so you can't get rid of that one although you could move it.
There's also normally a B junction (SM-JC41) placed inside the frame near the BB which I think is just 4 identical sockets and a signal repeater so I'm not sure you need it if you can connect everything into the A junction.
If you did that you would end up with 3 wires connecting the battery, shifter and RD directly to the A junction but I'm not quite sure where you would put the A junction to minimise total cable length and keep access to the charging port.
Given the B junction only costs about £20 I think I'd just fit one and be done with it.
You also need an overpriced Di2 charger and a selection of extra cables for when you've realised you've measured the bloody thing incorrectly and the run is 5cm longer than expected.
I ordered one cable of every length from Wiggle and returned the ones I didn't need apart from 800mm which was out of stock. Bet you can't guess which cable I needed.
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inappropriate_bike
Very soon I'll be running a 1x11 ultegra setup on my TT rig, and will also end up with a scuffed but functional 6870 rear mech. It would be nice to exchange out the mechanical shifters to clean up the front end in terms of cabling, and it appears you can get just the RH aero bar end shifter for about £60.
Junction box, battery and cables, do I need anything else? Will have to find a dummy bar end that resembles the 6871 shifter as well I guess. Do I even need a junction box if it's just 1x11?