Minimise backlash in DC geared motor
Why don't you use a control loop to integrate out the count error? You want to stop at 2000 and without a controller it stops at maybe 2010. If you had a feedback system it might overshoot up to 2016 but the feedback would bring the output shaft rapidly back to position 2000. 

Can you live with this type of overshoot? More sophistication can be incorporated so that the motor begins to decelerate as position 2000 is reached. A 3 term controller might be what you need and the basic overshoot could be possibly halved or more.

However, if the optical encoder is not on the output shaft then it won't work.