I have ordered the parts needed to modify the main board. I am not sure yet which method will be used for the driving of the LEDs and switches, so I have ordered sufficient parts to be able to test two options.
The first option is the lazy one. I will use an Arduino Mega board. The Mega uses a more powerful processor than the Arduino Uno and, more importantly, provides many more ports for input and output connections. The board is about twice as expensive as the standard Arduino board.
The second option is to emulate, sort of, the method used by Behringer to control the input and outputs on the FCB1010. The method is called multiplexing. The trick is to use additional components to interface with the LEDs and switches that allow less pins to be used on the Arduino.