A large source of noise in the system is the RC signals; they are both sensitive to noise, and cause noise in other circuits. According to the futoba manual:
-The receiver antenna should be seperated from other wires.
-To reduce noise in the motors "noise suppression capacitors" can be utilised.
-The RC receiver was moved to the back of the boat to isolate it from the rest of the system. This has significantly reduced noise levels.
-Moving RC to the back did not increase range enough. probably need a new transmitter and reciever. The control was moved to a xbee based solution.