Go Back to Basics, valves checked and adjusted, exhaust clamps tight with no leaks / no blowing, check colour of plugs are any black indicating running rich which can be caused by sticking butterfly flaps in throttle bodies ? replace plugs if necessary, air filter changed / clean? start bike, squirt wd40 around rubber seals of throttle bodies, if engine idle changes you have an air leak, split hose or perished throttle body seal, if have access to a g911 diagnostic tool, reset adaptations, check throttle bodies cable free play (5mm or so), if have g911 tool synchronise throttle bodies using a "carbtune" vac gauge, if cannot synchronise throttle bodies and vac readings are way out, remove throttle bodies and clean out any debris / sludge with carb cleaner, supermarket fuel with ethanol in gums up the butterfly flaps in the throttle bodies, causing flaps to stick and make the engine run rough and also makes synchronising impossible. When that is completed use g911 and view real time data, especially look at each cylinder temperature (both should be within 3 or 5 deg c of each other, look at the lamda sensor (O2) readings, they should be similar. If no g911 available, suggest remove and clean throttle bodies, refit, check the throttle cable cams move easily, adjust each throttle cable so that you can feel the butterfly cams move slightly at the same time for each cylinder whislt opening and closing throttle twistgrip about 10mm on the handlebar, this should enable throttle synch close enough to have the engine run much smoother. If in doubt take to a reliable mechanic. If the O2 sensors are faulty i have found that car ones may fit if the same thread, but you would need to cut the wires and change the electrical connectors over. Regards Steve
Quick check, lay down under the bike and locate the throttle body cams (wherethe cable fits in) turn the cam gently with your fingers and feel how tight it is (after taking into account the spring tension) compare to the other throttle body, the cam should turn easily with not much force, you can usually "feel" if the cam is stiff to turn, this indicates evaporated petrol in throttle body has left bio fuel debris behing causing the butterfly throttle flaps to stick. This is the main cause of rough running of these engines after using cheap petrol. If you clean the throttle bodies out, empty fuel tank if possible and use shell v power. Most expensive petrol is actually the cheapest, more power, more mpg, and clean fuel lines and clean throttle bodies.