I think maybe you received something other than an XR650L shifter. XR600R or XR650R maybe? Anyway, I recently installed an MSR XR650L shift lever on mine, and it sticks significantly further away from the case than the stock KLX250S lever. In fact I tried a little bit to bend mine closer to the stator cover to close up the gap. And from any pictures I've seen of the MSR XR650L lever installed on the KLX, the situation has been the same...it sticks farther from the stator cover than stock. Whatever the case, I found that it is much easier to shift now than with the OEM lever.