Just out of curiosity, how big is the rover?
I don't see where a CAN bus fits in. If I were you, I'd get a small computer (Mini ITX / Micro ATX) and link it to an Arduino via USB; there are lots of small options out there that can be powered with 12V. Let the Arduino control the motors, encoders, rotating cameras/etc. and the computer to handle the navigation, camera data stream, and communications. Looking at the cRio you mentioned I can see where you'd want to get away from that ($3K!).