This is why I originally found this forum. When I first got my Rebel, I found it uncomfortable to get my toes under the shift lever, so I moved the lever a notch on the shaft. That changed the angle of the linkage, and no amount of adjustment would let it shift as smoothly as the stock position. There is a mark on the end of the shaft that lines up with a mark on the lever to verify the stock position. I eventually learned to shift without getting my whole foot under the lever, and got comfortable with the stock position.
'09 Rebel 250
Loud ties save lives.