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This is not too difficult if you are at all handy with a soldering iron. If you are cutting and splicing you may decide not to use a junction box in the frame, and simply join all the ends together and cover with heatshrink. That way you only need to purchase half as many of the ridiculously expensive cables.
Don't forget to include an external junction between the frame and the handlebars.
Reading into it more I'm assuming the Di2 wires (2mm) would fit through the holes (drainage and bottle boss) but the plugs (5mm) wouldn't ? So that would mean cutting off the plugs and then soldering them back on after routing?