@mbellon, the stepper board (in the Nomad Classic at least) is 3-axis and all 3 axes are in use. 
The board in the Shapeoko3 has four drivers, but two are slaved for the Y axis. But even if it were reconfigurable it would not help me. My gearmotor is actually a servo.
I’m thinking the easiest way to implement rotary indexing might be to clamp a 5C collet block to the table against pins to register in the X and Y axes. The 4-sided block would give 90-degree increments, done manually in between the individual gcodes. The 6-sided block would need a tall fence to register in Y, but would give 60-degree increments.
http://www.shars.com/products/toolholding-workholding/collet-fixtures/5c-collet-block-set is a typical set.
Even the Shars block is claimed to be within .0005" squareness, so finding the axis in Y and Z would be very easy–edge find the block, touch down in Z and adjust each coordinate by half the block’s size.
I’ll need to add my voice to the requests for Rob to implement round stock when doing a 4-axis part…
Randy