Check out http://www.interspec.org/rovs
Russell Coffield runs these sites and he is a fellow ROV pilot/designer and friend of mine. He has a vehicle called a SeaMonkey running an Arduino Control system that he and the University of Victoria have been working on. He's a good resource and is looking for collaborators.
If you have not already found the code that you need, try here: ROV code
TCIII ArduRover2 Developer