You may want to check the position of your valve. IF you disconnected the cables, there isnt anything keeping the valve open. Basically you may be restricting your flow. I removed an exup valve motor from my R1 and then safety wired the valve butterfly all the way open. Is your bike running hot? I havent seen the R6 Valve yet since i built the R6 piece by piece I never had the stock can... Just bought a Graves SS Full pipe.
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