I don't think that you are allowed to have two EW-90's (A and B) in the system at the same time. I haven't tried it myself but none of Shimano's charts or manuals say that it will work.
Hmmmm... good info. The thing that made me think it would work was that I read a post from a guy that said he kept a spare EW-90A and 300mm cable and he'd plug it into his RD to charge the system.
You could use a pair of EW-JC41's or EW-JC130's to combine the shifter wires into a single wire in the downtube. The JC41 is small enough to fit inside of bars and bar extensions (I have done it) so they can be hidden. The other thing to consider is that the 6871 wires are permanently attached to the lever so if the length is wrong you will need additional wires and junctions. Take a look at the attached file which is an excerpt from the technical manual.Di2TT Wiring.JPG
I wasn't aware of that aspect of the 6971 shifter levers. Hopefully they'll work, if not, I may be forced to run some of the system external.
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