AngeloGomes:
the main problem is the motor displacement is not reproducible when it rotates back and forth sometimes.
If you put the encoder on the output shaft that you want to position, then you will be avoiding the backlash.
Place a constant load on the output shaft for the motor to work against, such as a rubbing device in contact with the output shaft.
Look for encoders with many thousands of steps per revolution, not 360 or 720.
5000 counts per revolution will give 5000/360 = 13.88 counts per degree.
0.072 Deg resolution.
Also you do not need to have the encoder connected directly to the output shaft.
It can be on another shaft driven by the output shaft, that has the required gear ratio to give your precise encoder outputs per degree.
You need to talk with encoder distributors of SICK, IFM, Turck, industrial encoders, they will be expensive, but that is what you pay for precision/consistency.
If you chat with the right sales rep or technician that is is turned on to this sort of thing, you may have some quick success.
ANOTHER solution, you have the output shaft/disk lock into mechanical detents that are 1 deg apart, no need for precision encoder just something to get you into the ball park and the detent or locking pin will pull the shaft to exactly integer degree positions.
There is a servo resolver solution, but that is very expensive and has some specific hardware requirements.
Just some thoughts.
Tom.. 
(PS read my side bar to this post.)