Yeah, that's what I had with my 996 a few Years ago: would'nt idle well after I installed open mufflers and set timing and squish. Closing the Airtubes half a turn and almost opening the CO-trimmer fully and it ran awesome.
This is why I have the same guess on this bike, but unfortunately, there is no CO-trimmer anymore!!
Does anyone know, if trimming via the PCIII is working in that area?? (1000-2000rpm's)