Why is the butterfly valve connected in the first place? Something does not sound right. I installed it myself and removed the servo motor and valve. It isn't needed for the akra system and should not be throwing any codes at all. If it's not a big deal to you, then live with it. If it was me, I'd go back n tell them to learn how to install the exhaust and follow some simple instructions.
did you get a feeling that the bike has less power with this exhaust? I can probably feel it, I can also feel it is considerably smoother