I know Seth hasn't replied here yet, but I'll weigh in. I forgot to update this thread to say that I eventually did merge the changes into polargraph_server_a1, albeit in a slightly different form.
You need to change the first set of #defines in polargraph_server_a1.ino to make sure that UNL2003_DRIVER is the only line that is not commented out:
// Using discrete stepper drivers? (eg EasyDriver, stepstick, Pololu gear),
// choose SERIAL_STEPPER_DRIVERS and define your pins at the bottom of 'configuration.ino'.
// Using a signal amplifier like a UNL2003?
Then you need to comment out all of the #include lines at the top of in configuration.ino that would usually load the adafruit libraries.
The bit you're interested in is the motor declarations:
AccelStepper motorA(8, 6,8,7,9);
AccelStepper motorB(8, 2,4,3,5);
Those numbers (6,8,7,9 and 2,4,3,5) are the arduino pins that Seth used to wire up the UNL2003s.