Hi Curtis,
Sorry to hear this. The max allowed motor supply voltage is 48V. 52V is clearly over spec but wouldn't have expected that to be enough to cause the failure. What kind of power supply are you using? Regulated or unregulated? Is it isolated from earth/frame GND?
Having no +5V would keep the FETs disabled with no current flow, but the driver chips would still be susceptible to over voltage.
Having the voltage Clamp set to 25V would have caused the voltage clamp to fail or give up quickly so the voltage would go to 52V.
Regarding:
#1 - that is bad. Even with no jumpers installed the supply should be clamped to 49V
#2 - reversing + and - on a stepper will just reverse the direction it rotates. It should not cause any other problem.
#3 - the peak unloaded voltage should be 48V or less.
What are your motor specifications?
Are you sure your wiring was correct? Did you check with an ohm meter from coil to coil and from coils to GND?
Regards