I purchased a used 2009 CRF450R, in Sept. of 2017, which was used for flat track, as I am using it, also.
I have been inspecting and freshening the engine this winter, and as I was putting the bottom end back together I discovered that the Gearshift Drum installed appears to be from a 2013-2016 CRF450R; the left end of the Gearshift Drum is flat with a small hole in the center, it does not have the raised collar with the notch in it, and the Gearshift Drum's left end, which the 2009 Gearshift Drum has, which accepts/engages the Pin on the Gear Position Switch's rod.
I did check continuity as described in the Service Manual, but did not note exactly, what position the Switch's Pin was in before I began moving it and noticing continuity and open. I recall that it tested as described in the Service Manual; 1st and Neutral = ground-light green/red, 2nd = ground-gray.
Now, my thinking was ... "the Gearshift Drum has no way to 'actuate' the Gear Position Switch, as it's end is flat/flush, no groove/notch. .. So, the Switch is basically, 'open circuit', not sending anything to the ECM. The switch is now, basically, a 'plug'." .. "I can eliminate the wires from the Gear Position Switch to the Main Wire Harness; one less set of wires to deal with." ... So, I cut the wires off of the Gear Position Switch, Dremel, cut off the switch's rod/pin and applied a thin coat of Yamabond to the Switch's inside, face.
Given the fact that I did not make note of the position of the switch's rod/pin when I removed it, if either of the wires are not connected to the harness/ECM, is this going to affect Fuel / Ignition / Starting? .. Given the fact the Gearshift Drum can not actuate/engage the Gear Position Switch, I would think I would not want the switch's position to be Permanently/Constantly set in either of the 1st-Neutral or the 2nd gear positions. So, unplugging it, [or even, eliminating the wires from the switch as I did], should be like the switch's position being in 3rd-5th gear. ... Hoping it will not make it more difficult to Kick Start or affect idle or performance. ... I mean, I wouldn't want any 'signal' to the ECM that the transmission is constantly, in 1st, Neutral or 2nd.