I think this is the bit that I'm missing. Where is that simple setting? I can't see it documented anywhere. I'm probably just blind.

IIRC, you don't actually need to modify the arduinoboy at all. It's been a while, but I seem to remember being able to use a dual ended link cable, one end plugged into a GBA and one end into a DMG, both running mGB, and both would receive notes. I did not try with the modified midi channel rom though.

You'd need a customized arduinoboy running this code and using a modified pinout to support two Game Boys. However, since mGB has a simple setting for changing the midi channel offset, you don't need to be running a custom ROM or anything.

The pinouts you need are here:

int pinGB1Clock     = 0;    // Analog In 0 - clock out to gameboy 1
int pinGB1SerialOut = 1;    // Analog In 1 - serial data to gameboy 1
int pinGB1SerialIn  = 2;    // Analog In 2 - serial data from gameboy 1

int pinGB2Clock     = 3;    // Analog In 3 - clock out to gameboy 2
int pinGB2SerialOut = 4;    // Analog In 4 - serial data to gameboy 2
int pinGB2SerialIn  = 5;    // Analog In 5 - serial data from gameboy 2

int pinMidiInputPower = 4; // power pin for midi input opto-isolator

int pinStatusLed = 13; // Status LED
int pinLeds[] = {12,11,10,9,8,13}; // LED Pins

int pinButtonMode = 3; //toggle button for selecting the mode

Does anyone have any experience of running two gameboys through the Lowtoy arduinoboy, or anything similar?

"As bonuses these boards have a double input to control TWO gameboys. This can be achived with this program for the Arduino, developed (and currently being improved) by Luis Gonzalez aka Hadesbox."
https://github.com/hadesbox/dualarduinoboy
http://www.lowtoy.com/portfolio/arduinoboy-shield/

What I'd like to do is run mGB on two different Gameboys on MIDI channels 1-10. This seems to imply that to do that I'd need a custom version of mGB. Is that crazy talk?

I definitely could use two arduinoboys, but it would be nice not to have to buy anything else.