The shifter stops would not cause that. Mis-adjusted stops will improperly limit the travel of the shifter keeping the transmission from fully engaging a gear and causing it to pop out of gear.
It seems that only the factory shifter has a rubber isolator between the handle and the shifter base. This rubber makes the shifts rather sloppy, but it does hold back noise and vibrations!
Unfortunately, driving with your hand on the shifter to make it quiet will also put a little pressure on the plastic fork pads and encourage them to melt down as you drive...