Well I confirmed that I have a power supply issue. I’m seeing a nearly 2 volt drop in the 12 volt supply when stepping. The onboard regulators are doing their job, but the wall wart I’m using doesn’t appear to be able to deal with the instantaneous load of the stepper motor. I’ve confirmed this by connecting a bench power supply with alligator clips and seeing a much more stable 12 volt supply during head movement operations. Unfortunately in the process, I somehow fried my AVR flash programmer. Until I build or buy a new one, further debugging will be delayed. I will be able to work on designing the USB interface while I sort out the flash programming issue, though.