As a follow-up to this thread and about signal processing of the encoder signal, have a look at Optical Motor Shaft Encoder in Zumo with Signal Processing, there is as well a link to the Eagle files of that processing PCB.
We took that approach further and have created our own Zumo board with ARM processor on it and Arduino shield headers. The board includes the comparator circuit and works very well:
Details: https://forum.pololu.com/t/modding-the-zumo-encoders-wifi-gps-usb-and-120-mhz/7286/1
Erich