I had this experience once I picked up my 09 SERG and it was driving me nuts. Before I left Daytona, Jaybrake put on the prototype forward controls and it cured the problem instantly. I think it has something to do with the pressure on the inner cover then anything. If you adjust your foot shifter arms out a fraction of an inch it should cure this.
I think a big part of the problem is the effort it takes to overcome any friction in the system, which makes it too easy to shoot past neutral when everything finally starts moving. Of course, that friction comes from several areas. The linkage itself, as you noted, can add significant friction. Then you have internal trans friction at the shift drum, shift forks and the shift rings. Those are the parts that respond to better lubes. One other area that makes a huge difference is clutch drag. The old tactic of pulling the clutch, blipping the throttle, and then trying for neutral is based on the idea that the throttle blip will break the clutch plates loose. Same thing works for that clunk going into first, btw. Pull the clutch, blip the throttle, wait a few seconds, and then drop it into first with nary a sound or jerk.
Jerry