I just read throught the data sheet on their website. I didn't see anything about the Vref being set to 0 by default. It does tell you where to measure the Vref.
While not in the best place, it also says this.The potentiometer creates a voltage which is input to the drivers Vref
(Voltage Reference) pin. The Vref voltage is referenced to ground (GND) and can be monitored at the test points TPX,TPY and TPZ
The picture in the Data sheet clearly shows where these points are.The GND & Vcc (+5VDC) available on the right hand side of the board can be used to pull limit inputs high through a 10K resistor. It is not intended to drive other devices. This GND can be used for Vref set reference.
The data sheet also says to power the board, then adjust the Vref. And don't esceed 3.6V. Perhaps you exceeded the 3.6V by adjusting it with the power off?
I'd contact Jeff at Xylotex, his support is outstanding. If the board did get damaged, they can usually be repaired.
As for setting the microstepping, it seems prett clear in the data sheet. Jumpers for MS1 and MS2 are listed in a chart for the different microstep settings. They are labeled with a 0 or 1, with a note saying 1 means jumper NOT installed.