The emergency stop button should be connected to the two outer pins of the endstop connector.
You could omit the 12V step down converter if you common the negative outputs of the two power supplies and feed +12V from the bed heater power supply to the centre pin of the fan voltage selector block.
The Mosfet board isn't needed if you connect both PSU negative outputs to the negative VIN terminal of the Duet, and connect the bed heater between the positive output of the bed heater PSU and the BED- terminal of the Duet. If you do that then the bed heater LED will always be lit (brighter when the bed heater is turned on), but that won't do any harm.
