Yes there are lots of spare pins, many of them brought out on the expansion connector. See the Duet schematic for details. Note that the pin on the expansion connector immediately above the one that the IR probe is connected to is now used by the modulated IR and ultrasonic probes, sop I suggest you avoid using that one.
There is already a driver and output pins on the Duet for one PWM-controlled fan.
Large delta printer [miscsolutions.wordpress.com], E3D tool changer, Robotdigg SCARA printer, Crane Quad and Ormerod
Disclosure: I design Duet electronics and work on RepRapFirmware, [duet3d.com].
