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Good idea, but also sounds like a pita to then try and thread that through.
I'm thinking of putting the junction box on the stem anyway, as in real terms it'll make no difference. But it will mean there is more chance of me remembering to charge the thing! It should be quite neet, one shifter into each side, then cable from middle out and over headset top cap into hole, can tape that cable too as won't move.
Could you drill the extensions and put the wire running between them inside the base bar?