Funny you should ask. In what may amount to Slowtwitch blasphemy, I recently switched from a Cervelo S5 to a Cannondale EVO (our club is sponsored by Cannondale). As part of getting my components over to the Cannondale, I talked to my mechanic about getting the junction box off the stem. He ended up putting it under the seat tube bottle cage, where is remains readily accessible. But now my front end is clean! This was all inspired by Daniel Holloway, who saw my old S5 and was not impressed with my aero. Haha. He has his junction box in the BB of his Felt AR (he accesses the junction box by popping off the plastic under-BB cable guide), but I didn't have that option with my EVO because it's a di2-only frame without a cable guide under the BB.

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Amateur recreational hobbyist cyclist
https://www.strava.com/athletes/337152
https://vimeo.com/user11846099

Looks great. Can you go over the way the Di2 wires connect? I assume right shifter to left. Left shifter to junction box? Junction box to internal box (then battery, RD, FD)?

I think you nailed it. That sounds exactly as my mechanic explained it to me. And I have the satellite shifters there as well, so we didn't have to give those up!

I used to build up my own bikes but these days it's better for matrimonial harmony to leave that to my mechanic. And he's a good buddy so it give me an excuse to go see him.

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Amateur recreational hobbyist cyclist
https://www.strava.com/athletes/337152
https://vimeo.com/user11846099

Maybe you could help me on this (or anyone else), because I am slightly confused. The last picture of the FD. I see the wire coming into the front junction box. But then I see the one leaving and instead of going back into the side to the internal junction box, it looks like it goes to the FD? Is that right?

I'm not entirely 100% sure on how the setup of Di2 needs to be, but do the wires for the FD/RD/Battery/front shifters have to all enter into the SM-JC41 junction box for the system to work? Or does that not matter.

Doesn't matter. All the components just need to be connected - they can all be daisy-chained or come back to the junction, or some combination.