Finished rewiring my arduino mega shield and plugged in the stepper controller and it worked great. Had to make one adjustment to one of the resistors. Had to change R2, the pullup resistor used with the jumpers to select the microstepping from 100K Ohms to 10K Ohms. There are 100K Ohm pulldown resistors built into the pololu controller, and I pull down MS1 with a 100K Ohm resistor for when that pin isn't jumpered. When I had everything plugged up, it only did full steps, no matter what combination of jumpers I set. So I replaced the resistor on the pullup side to 10K Ohms and now all the microstepping options work great. Now to solder up 3 more boards and hook things up to my repstrap.
I've got 15 boards to sell, if you want one, let me know.