A couple of more things to check:
Do you have the latest fuel map; I believe it is 4533V796. I know my dealer up graded mine from the original. You can check the number with GuzziDiag, or ask your dealer.
Are your plug caps making good connection to the plugs? Are the caps shorting to the head? This is a known problem. Besides poor running, another symptom is color (brown, or blue if it's real bad) on the mufflers - fuel that did not burn in the cylinder is burning in the catalytic converter. One of my mufflers was turning brown. I checked the plug connector by first pushing it on further. The one with the brown pushed on further - felt like it moved an eight inch or more. The engine runs better now.
Dan
The top 6-8 inches of the pipes are solid blue... then everything is perfectly chrome beyond that. It was that way when I bought it.
I just got off the phone with my local dealer/service shop and they confirmed that the original factory warranty stays with the bike regardless of owner. I will be making an appointment as soon as their service writer gets in.