I built a walking (biped) robot and had trouble with motor noise causing the A/D signals to vary. (I use two A/D inputs to read pots coupled to the legs for position information.) Adding .1uf caps from each motor lead to the motor's case solved the problem.

My motors are the cheaper hobby motors used with the Tamiya double gearbox. If you are using the Pololu serial motor controller they recommend the caps too. I use an analog H bridge and still had noise issues even with seperate motor and logic batteries.

I don't know if it will help you but it is something to try....

By the way, you did an excellent job on the project, I hope it works out.
--John