The only way to shield the encoder was to make an aluminium disc plate. This was screwed into the back plate of the motor with small Allen screws. The encoders were then  screwed into the aluminium plates.

 

To get correct alignment I made a small top hat bush, which fitted over the motor shaft and used a punch guide.

 

I deliberated long and hard about taking the back plate off the stepper motor.

 

After a lot of research I spoke with several suppliers, who re-assured me if I was very careful!  , it would not upset the motor. If you do this, treat the motor with great care and always make sure the back plate goes back together in exactly the same place.

 

The encoder wheels also had to be reamed carefully in the lathe to fit my shafts. When fitting them, the position in the reader head is quite critical, and some took several attempts to get right and working correctly.