I accidentally shorted motor outputs 3&4 to +5v leaving my Quadcopter with only 2 working motor outputs(1&2). Outputs 5&6 are still operational and was wondering how to go about re-routing outputs 3 to 5 and 4 to 6 so i can still use this board to fly my quad.

I'm using the ArduPilot Mega (the red & blue boards) with Firmware 2.5.3 Mission planner 1.1.69

I can't find any setting to do this so i assume i will be building the firmware using the supplied libraries, any help in pointing me in the right direction would be great.

Eclipse is installed, i have the source, what else do i need?

thanks