Have you had a check under the seat / by the throttle body for any disconnected or damaged vacuum hoses? There should be two hoses that go to the rear charcoal canister (the big boxy thing, one hose is to the engine, one is to the fuel tank), and from memory there is one by the throttle body where a Scottoiler joiner thing was on my bike. I would have expected it to throw a code if this was the problem, but worth checking and costs nothing.
