My R1200GS never idled smoothly or ran particularly smooth since I bought it. At the 600 mile run-in service, the heads were supposed to have been re-torqued and the valves set. OK, it ran a little better but still not how I thought it should.
During my 6000 mile (10,000 KM) service, I discovered the valves on the left cyclinder had almost no clearance. Not wanting to be a whiner to my dealer, I called them and carefully asked if there is anything they know about that could cause this. Their answer was for me to schedule an appointment and bring the bike in for the regular service, about $400 USD. No thank you.
After carefully rechecking the clearances on the right cyclinder and making sure the engine was rotated to the correct position to set the valves on the left cyclinder, I set everything to factory spec.
Now the engine runs smoothly and fuel consumption is significantly better, > 50 mpg. Connecting a twinmax syncronizer to the throttle bodies, everything is perfect, no further adjustments were needed.
Makes me think everything was not set properly during service sessions by the dealer. I understand they work on many different machines each day and a person can get interrupted and not do everything correctly. I can take my time and insure things are set properly. Setting the valve clearance is one of the really simple tasks. Checking and balancing the throttle bodies is equally simple yet results in major benefits in engine performance. It pays to be careful. Now my engine performs as it was designed to do.