OK... I got the stuff yesterday afternoon and have a chance to do a dry-fit this morning and get an idea about how the wires will layout. It appears as if the cables from the shifters on both the extensions and base bar will all be long enough to get to where I need them to go inside the head tube. I'm using Cameron Piper's ExploShiv
as a guide.
You can see in the picture below that he has the Di2 wires coming out of the back of the aero bars an into the top of the stem (where the read brake line should be coming out). The holes inside the aero bar mounts are a touch small, I'm measuring 4mm and I've read that the Di2 wires need 6mm clearance, so I'm hoping to put a small drill bit in and take out just enough material to clear. The good part is, I have a bunch of spares that I can test on first
In the pic below, you can see that they drilled small holes in base bar to route the brake lever Di2 buttons into the bar, so the internal routing is handling the Di2 wires and the brake cables. This will be a tight fit, but should work.
In this photo below, you can see that he's pulled a bunch of the Di2 guts from inside, and re-routed them back through the brake hole in the top of the stem (you can read why its like this in the link above) but this photos also clearly shows the Di2 cables coming out of the aero bar mounts and you can also see that the back of the stem cover has been trimmed. I believe this is to allow the rear brake cable as well as the Di2 wires, to go from under the stem cover, into the hole in the head tube. He's using a 5-port junction box, which I'm guessing is normally stuff into the head tube and not accessible, so he must be charging via a separate junction box that he plugs into one of the derailleurs.
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