We finally found the hardware design (mechanical and electrical) which we are going to stick with for some time. The main problem was power supply which was affected by the noise from motors. Using SparkFun's DC/DC converter breakout board and logic level converter we manage to isolate the noise from the main board. Here is how it looks like now:
As you can see on the first picture, we are not using TrainerBoard for now. Instead we decide to generate two PWM signals to control steering and acceleration directly from BeagleBoard using GPIO pins available on expansion connector. Level converter is used to convert +1.8V to +5V required for standard RC controller and servo.
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