Pypilot motor controller

[NahanniV]

...
It has a lower idle current because there is only one uC now, so this saves power.  In the future I may replace the 5v regulator on the arduino with a switching one to further save power.
...

I think you are heading in the right direction here, adding a simple "H" bridge, But:
Would it not be simpler and more efficient to get rid of the Arduino completely and just add an ADC to the RPi ?

Come up with a drip proof box with a heat sink and terminal strip for connections and you would have a very simple and easy to install autopilot with better functionality than commercial units that cost thousands of dollars. 

Cheers,
JM.