Hi Hardy,
You are right, the S12ZVM was not designed for applications with encoders (TIM module is the simple timer). The most of the applications with S12ZVM are sensorless or applications with hall sensors.
I would like to recommend some of the MCUs from MPC5xxx family or S32K (PREPRODUCTION) for your application with the incremental encoder.
For example:
http://www.nxp.com/products/microcontrollers-and-processors/power-architecture-processors/mpc5xxx-5x...
http://www.nxp.com/products/microcontrollers-and-processors/arm-processors/s32-arm-processors-microc...
I hope it helps you.
Have a great day,
Radek
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