REWIND: yes, you need to be able to rewind. That is an interesting feature by itself. Any transport that will be useful in a production environment needs rewind capability. My transport is fully controllable for speed and direction. Any film you are going to transfer needs some setup for color and exposure, and then rewind to your start position for recording.
Sprocket position adjustment. If you look at the Muller, they used linear stages to move the sensor and the light. My plan was to build both the Keyence laser and the reflector into a platform that is mounted on a linear stage. Then motorize the stage with a stepper and control its position with presets for different guages or film types.
For missing sprockets, you can code an alternate trigger in software that fires the camera/light array if pulses are not delivered from the laser. if you keep track of the timing of the laser delivered pulses the code could be substituted at the same rate. Not that I actually know how to do this, but theoretically.
About the transport. One thing to note is the need for a rigid transport. The whole platform may not need to be rigid, but the core gate, light, sensor, and camera spine must be very rigid to isolate it from any vibrations. If any motion is induced from the rest of the transport, the images will be unstable.