Are you using the facility to have the firmware level the bed by adjusting the Z leadscrew motors individually? If so, then the locations of the probe points are in the G30 commands in the bed.g file. If you are not using that facility, then you need only run mesh bed probing.
Shorting fan pins blows the mosfet, and may also blow the 1A fuse (on Duet revision 1.03 or later) or the trace linking VIN to the VIN side of the fan voltage jumper selector block. If the fan still works when you plug it into one of the always-on outputs, then only the mosfet is blown.
