I managed to get the shaft mounted optical quadrature wheel encoder http://www.pololu.com/product/2591
to work inside the Zumo chassis.
As the encoder produces an analog signal, and we have seen that it can be heavily impacted by light and other factors, we decided to create a processing PCB which transfors the analog signal into a clean and calibrated digital quadrature signal. With this, we are able to accurately process the signal of the 1:75 Micro Metal Gear Motor at full speed with the 3-tooth encoder. Best of all: the Zumo Bot can perform per software an auto-calibration
With the hope that this might be beneficial for someone else, all the details, schematics and sources are posted here:http://mcuoneclipse.com/2014/03/08/processing-the-pololu-motor-shaft-encoders/