@chrismbp Okay, that sounds more like the 12V regulator has either failed or is being shorted out. I'd try disconnecting everything from the board (in case it's a short) and see if it helps. I'm not sure if the 5V or 3.3V regulators are fed by the 12V regulator, but if could also be one of those has failed.
As to the cause, I'm not sure. Changing to stealthChop, and having V1000 as the changeover speed to spreadCycle, might have caused the clunk when moving to higher speed travel moves. It's possible if this was fast enough, it may cause an overcurrent situation. See https://docs.duet3d.com/User_manual/Connecting_hardware/Motors_tuning#configuring-stealthchop
A jerk occurs when switching at higher velocities, because the back-EMF of the motor (which rises with the velocity) causes a phase shift of up to 90° between motor voltage and motor current. So when switching at higher velocities between voltage PWM and current PWM mode, this jerk will occur with increased intensity. A high jerk may even produce a temporary overcurrent condition (depending on the motor coil resistance). At low velocities (e.g. 1 to a few 10 RPM), it can be completely neglected for most motors. Therefore, consider the switching jerk when choosing TPWMTHRS. Set TPWMTHRS zero if you want to work with StealthChop only.
It's possible this is what happened. @dc42 might know better the effects of this. Let's see if there's any life in the board with everything disconnected, and go from there.
Ian